From aebbce71060aa1e9f057be19954f6d8f39e7e2a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Nov 2013 23:45:22 +0100 Subject: [PATCH 001/992] add easyconfig file for Vampir --- .../v/Vampir/Vampir-8.1.0-linux-x86_64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb new file mode 100644 index 0000000000..933876ab64 --- /dev/null +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb @@ -0,0 +1,32 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock='Binary' + +name = "Vampir" +version = "8.1.0" +versionsuffix = "-linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The VAMPIR software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vampir-%s-standard%s-setup.bin' % (version, versionsuffix)] + +install_cmd = "./vampir-8.1.0-standard-linux-x86_64-setup.bin --silent --instdir=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/vampir", "doc/vampir-manual.pdf"], + 'dirs': [] +} + +moduleclass = 'perf' -- GitLab From c960524a9568dfad8922bc648a0563776395f0d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Nov 2013 21:39:37 +0100 Subject: [PATCH 002/992] get rid of hardcoding version/versionsuffix --- easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb index 933876ab64..7b467d1272 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb @@ -20,9 +20,9 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['vampir-%s-standard%s-setup.bin' % (version, versionsuffix)] +sources = ['vampir-%(version)s-standard%(versionsuffix)s-setup.bin'] -install_cmd = "./vampir-8.1.0-standard-linux-x86_64-setup.bin --silent --instdir=%(installdir)s" +install_cmd = "./vampir-%(version)s-standard%(versionsuffix)s-setup.bin --silent --instdir=%(installdir)s" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], -- GitLab From e690eec2d9aa50c46603d8801860b05023005eea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Dec 2013 17:27:45 +0100 Subject: [PATCH 003/992] add easyconfig files for ncdf/ncdf4 for R 2.15.3 + dep easyconfigs --- ...HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb | 31 +++++++++++++++++++ .../n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb | 29 +++++++++++++++++ .../ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb | 29 +++++++++++++++++ .../netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb | 21 +++++++++++++ 4 files changed, 110 insertions(+) create mode 100755 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb create mode 100644 easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb create mode 100644 easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb create mode 100755 easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb new file mode 100755 index 0000000000..1b26514524 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb @@ -0,0 +1,31 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management + of extremely large and complex data collections.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +zlib = 'zlib' +zlibver = '1.2.5' +versionsuffix += '-%s-%s' % (zlib, zlibver) + +dependencies = [ + (zlib, zlibver), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb new file mode 100644 index 0000000000..a5891cb70a --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf' +version = '1.6.6' + +homepage = 'http://cran.r-project.org/web/packages/ncdf4' +description = """This package provides a high-level R interface to data files written using Unidata's netCDF library + (version 4 or earlier), which are binary data files that are portable across platforms and include metadata + information in addition to the data sets.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [ + 'http://cran.freestatistics.org/src/contrib', + 'http://cran.r-project.org/src/contrib/Archive/ncdf', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '2.15.3' + +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.2.1.1', '-zlib-1.2.5'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb new file mode 100644 index 0000000000..dc58f15fe2 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.10' + +homepage = 'http://cran.r-project.org/web/packages/ncdf4' +description = """This package provides a high-level R interface to data files written using Unidata's netCDF library + (version 4 or earlier), which are binary data files that are portable across platforms and include metadata + information in addition to the data sets.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [ + 'http://cran.freestatistics.org/src/contrib', + 'http://cran.r-project.org/src/contrib/Archive/ncdf4', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '2.15.3' + +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.2.1.1', '-zlib-1.2.5'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb new file mode 100755 index 0000000000..5c53c8bf57 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb @@ -0,0 +1,21 @@ +name = 'netCDF' +version = '4.2.1.1' +versionsuffix = '-zlib-1.2.5' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [ + ('HDF5', '1.8.10', '-gpfs%(versionsuffix)s'), + ('Doxygen', '1.8.2'), +] + +moduleclass = 'data' -- GitLab From 4b67659ba2376c552748309970b0583135fb85af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 16:58:30 +0100 Subject: [PATCH 004/992] add patch file required for correct CUDA-aware OpenMPI v1.7.3 build --- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 2 ++ .../OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch | 16 ++++++++++++++++ 2 files changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index 9198983666..4ddc24fe07 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -9,6 +9,8 @@ toolchain = {'name': 'gcccuda', 'version': '2.6.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +patches = ['OpenMPI-%(version)s_common-cuda-lib.patch'] + builddependencies = [ ('Automake', '1.14'), ('Autoconf', '2.69') diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch new file mode 100644 index 0000000000..4ba9ebab68 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch @@ -0,0 +1,16 @@ +see http://permalink.gmane.org/gmane.comp.clustering.open-mpi.user/20404, +patch obtained via https://svn.open-mpi.org/trac/ompi/changeset/29762 +Index: /branches/v1.7/ompi/mca/pml/ob1/Makefile.am +=================================================================== +--- /branches/v1.7/ompi/mca/pml/ob1/Makefile.am (revision 29624) ++++ /branches/v1.7/ompi/mca/pml/ob1/Makefile.am (revision 29762) +@@ -68,4 +68,9 @@ + mca_pml_ob1_la_LDFLAGS = -module -avoid-version + ++if OPAL_cuda_support ++mca_pml_ob1_la_LIBADD = \ ++ $(top_ompi_builddir)/ompi/mca/common/cuda/libmca_common_cuda.la ++endif ++ + noinst_LTLIBRARIES = $(component_noinst) + libmca_pml_ob1_la_SOURCES = $(ob1_sources) -- GitLab From b9b0d39cf997b2d2d74d557f36a2a58ff8125d63 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 4 Feb 2014 16:38:19 +0100 Subject: [PATCH 005/992] CONTRAfold-2.02-goolf-1.4.10.eb --- .../CONTRAfold-2.02-goolf-1.4.10.eb | 31 +++++++++++++++++++ .../c/CONTRAfold/contrafold-gcc47.patch | 20 ++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch diff --git a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb new file mode 100644 index 0000000000..815406dfba --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'CONTRAfold' +version = '2.02' + +easyblock = 'MakeCp' + +homepage = 'http://contra.stanford.edu/contrafold/' +description = ''' CONditional TRAining for RNA Secondary Structure Prediction ''' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_'))] + +patches = ['contrafold-gcc47.patch'] + +start_dir = 'src' + +files_to_copy = [(['score_prediction', 'contrafold', 'score_directory.pl',\ + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/score_prediction', 'bin/contrafold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch b/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch new file mode 100644 index 0000000000..d484c76bfd --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch @@ -0,0 +1,20 @@ +--- contrafold.orig/src/Makefile 2008-08-14 02:08:30.000000000 +0200 ++++ contrafold/src/Makefile 2014-02-04 13:51:29.041589171 +0100 +@@ -1,6 +1,6 @@ + CXX = g++ + +-CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall ++CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall -fpermissive + LINKFLAGS = -lm + GDLINKFLAGS = -lgd -lpng + +--- contrafold.orig/src/Utilities.cpp 2008-08-14 02:08:31.000000000 +0200 ++++ contrafold/src/Utilities.cpp 2014-02-04 14:09:09.082650184 +0100 +@@ -2,6 +2,7 @@ + // Utilities.cpp + ////////////////////////////////////////////////////////////////////// + ++#include + #include "Utilities.hpp" + + bool toggle_error = false; -- GitLab From 13b7f5c9ee8638fed92150ab57cdb6467b8320df Mon Sep 17 00:00:00 2001 From: Petar Forai Date: Mon, 10 Feb 2014 23:48:22 +0100 Subject: [PATCH 006/992] contrib blasr configs. --- .../b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb | 43 +++++++++++++++++++ .../easyconfigs/b/blasr/non-static.patch | 13 ++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/blasr/non-static.patch diff --git a/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..5663de6022 --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb @@ -0,0 +1,43 @@ +# With <3 for EasyBuild +# +# EasyConfig for BLASR: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +name = 'blasr' +version = 'smrtanalysis-2.1' + +easyblock = "MakeCp" + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" + + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +#like https://github.com/PacificBiosciences/blasr/archive/smrtanalysis-2.1.tar.gz for tag smnrtanalysis +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] + + +patches = ['non-static.patch'] + +files_to_copy = [(['alignment/bin/wordCounter', 'alignment/bin/printReadWordCount', 'alignment/bin/blasr', 'alignment/bin/sdpMatcher', 'alignment/bin/swMatcher', 'alignment/bin/kbandMatcher', 'alignment/bin/sawriter', 'alignment/bin/saquery', 'alignment/bin/samodify', 'alignment/bin/printTupleCountTable', 'alignment/bin/malign', 'alignment/bin/cmpPrintTupleCountTable', 'alignment/bin/removeAdapters', 'alignment/bin/tabulateAlignment', 'alignment/bin/samatcher', 'alignment/bin/sals', 'alignment/bin/saprinter', 'alignment/bin/buildQualityValueProfile', 'alignment/bin/extendAlign', 'alignment/bin/guidedalign', 'alignment/bin/pbmask'],'bin')] + + +sanity_check_paths = { + 'files': ['bin/wordCounter', 'bin/printReadWordCount', 'bin/blasr', 'bin/sdpMatcher', 'bin/swMatcher', 'bin/kbandMatcher', 'bin/sawriter', 'bin/saquery', 'bin/samodify', 'bin/printTupleCountTable', 'bin/malign', 'bin/cmpPrintTupleCountTable', 'bin/removeAdapters', 'bin/tabulateAlignment', 'bin/samatcher', 'bin/sals', 'bin/saprinter', 'bin/buildQualityValueProfile', 'bin/extendAlign', 'bin/guidedalign', 'bin/pbmask'], + 'dirs': [], +} + +makeopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' + +dependencies = [ + ('HDF5', '1.8.9'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr/non-static.patch b/easybuild/easyconfigs/b/blasr/non-static.patch new file mode 100644 index 0000000000..03b7b3f2bb --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/non-static.patch @@ -0,0 +1,13 @@ +--- common.mk.orig 2013-11-08 15:19:36.848815000 +0100 ++++ common.mk 2013-11-08 15:19:54.854217000 +0100 +@@ -24,6 +24,7 @@ + ifeq ($(shell $(CC) -dumpversion | awk -F '.' '$$1*100+$$2>404{print "yes"}'),yes) + CPPOPTS += -fpermissive + endif +-ifneq ($(shell uname -s),Darwin) +- STATIC = -static +-endif ++# Why oh why ... ++#ifneq ($(shell uname -s),Darwin) ++# STATIC = -static ++#endif -- GitLab From ee0ac46ff9ae257f194baf35407fd7aa23ae391f Mon Sep 17 00:00:00 2001 From: build Date: Fri, 28 Feb 2014 14:09:44 +0200 Subject: [PATCH 007/992] Contributing parallel version of ABINIT built with ETSF_IO to enable checkpointing --- .../a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 27 ++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..c1d2b559d8 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# +## + +name = 'ABINIT' +version = '7.4.3' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://ftp.abinit.org/'] + +configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' + +dependencies = [ + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), +] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] + } + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..7e1b945d47 --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -0,0 +1,27 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# +## + +name = 'ETSF_IO' +version = '1.0.4' + +homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' +description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" + +dependencies = [ ('netCDF', '4.1.3') ] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] + } + -- GitLab From 64bae018eaecad71608473c16bd9f0c97031b21c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Mar 2014 17:03:31 +0100 Subject: [PATCH 008/992] add easyconfig file for LAMARC + required patch file --- .../l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb | 23 +++++++++++++++++++ .../l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch | 10 ++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb new file mode 100644 index 0000000000..742fe0d215 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +name = 'LAMARC' +version = '2.1.9' +versionsuffix = '-headless' + +homepage = 'http://evolution.genetics.washington.edu/lamarc/' +description = """LAMARC is a program which estimates population-genetic parameters such as population size, + population growth rate, recombination rate, and migration rates.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://evolution.genetics.washington.edu/lamarc/download/'] +sources = ['%(namelower)s-%(version)s-src.tgz'] + +patches = ['LAMARC-2.1.9_Makefile-fix.patch'] + +configopts = "--disable-converter --disable-gui" + +sanity_check_paths = { + 'files': ["bin/lamarc"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch new file mode 100644 index 0000000000..74db39ff1c --- /dev/null +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch @@ -0,0 +1,10 @@ +--- lamarc/Makefile.in.orig 2014-03-19 14:25:08.261820031 +0100 ++++ lamarc/Makefile.in 2014-03-19 14:25:15.382031107 +0100 +@@ -1810,7 +1810,6 @@ + doc/html/genotype.html \ + doc/html/glossary.html \ + doc/html/growthmenu.html \ +- doc/html/forces.html \ + doc/html/index.html \ + doc/html/insumfile.2reg3rep.html \ + doc/html/insumfile.2reg3rep.xml \ -- GitLab From ae32b280a9f5cd19f8b2df995ee60303de9545ce Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 5 Apr 2014 16:41:37 +0200 Subject: [PATCH 009/992] AutoDock_Vina-1.1.2-linux_x86.eb --- .../AutoDock_Vina-1.1.2-linux_x86.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb new file mode 100644 index 0000000000..a27cf3bd19 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'AutoDock_Vina' +version = '1.1.2' +versionsuffix = '_linux_x86' + +homepage = 'http://vina.scripps.edu/index.html' +description = """ AutoDock Vina is an open-source program for doing molecular docking. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://vina.scripps.edu/download/'] +sources = ['%s_%s%s.tgz' % (name.lower(), version.replace('.','_'), versionsuffix)] + +sanity_check_paths = { + 'files': ["bin/vina_split", "bin/vina"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 2aab27e19259b38b61250c798f1897d07e5c2140 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 8 Apr 2014 23:21:18 +0200 Subject: [PATCH 010/992] Check-0.9.12-goolf-1.4.10.eb --- .../c/Check/Check-0.9.12-goolf-1.4.10.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb new file mode 100644 index 0000000000..e63d0852ef --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb @@ -0,0 +1,21 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = "Check" +version = "0.9.12" + +homepage = 'http://check.sourceforge.net' +description = """ Check is a unit testing framework for C. It features a simple interface + for defining unit tests, putting little in the way of the developer. Tests are run in a + separate address space, so both assertion failures and code errors that cause segmentation + faults or other signals can be caught. Test results are reportable in the following: + Subunit, TAP, XML, and a generic logging format.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'devel' -- GitLab From 38696b3ba189737da986398f408d49fa21b57cb7 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 9 Apr 2014 16:36:16 +0200 Subject: [PATCH 011/992] added FDS --- .../f/FDS/FDS-r18915-goolf-1.4.10.eb | 25 +++++++++++++++++++ .../easyconfigs/f/FDS/FDS_makefile.patch | 15 +++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/f/FDS/FDS_makefile.patch diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb new file mode 100644 index 0000000000..532468b97f --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -0,0 +1,25 @@ +name = 'FDS' +version = 'r18915' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """ + Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and + heat transport from fires. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +patches = ['FDS_makefile.patch'] +modextrapaths = {'bin': 'FDS_Source'} + +sanity_check_paths = { + 'files': ['FDS_Source/fds'], + 'dirs': [], +} +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS_makefile.patch new file mode 100644 index 0000000000..d9c7c2a315 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS_makefile.patch @@ -0,0 +1,15 @@ +--- makefile (revision 18916) ++++ makefile (working copy) +@@ -29,9 +29,9 @@ + + # General Purpose Rules + +-no_target: +- @echo \******** You did not specify a make target \******** +- @echo Please read the comments at the top of the makefile ++no_target: FCOMPL = $(F90) ++no_target: setup $(obj_serial) ++ $(FCOMPL) $(FFLAGS) $(LFLAGS) -o fds $(obj_serial) + + setup: + %.o : %.mod -- GitLab From 2178f44c0af1b92efed808dd242edaa2e7e04e26 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 9 Apr 2014 16:45:43 +0200 Subject: [PATCH 012/992] use mpi and add to path, not to bin --- easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb index 532468b97f..d49cfa69e6 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -8,7 +8,7 @@ description = """ """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCE_TAR_GZ] # just run make in the install dir @@ -16,7 +16,7 @@ skipsteps = ['configure', 'install'] buildininstalldir = True patches = ['FDS_makefile.patch'] -modextrapaths = {'bin': 'FDS_Source'} +modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { 'files': ['FDS_Source/fds'], -- GitLab From 570d6004b3a3dece9f0d4d2964b5a7576d211573 Mon Sep 17 00:00:00 2001 From: admin6 Date: Wed, 9 Apr 2014 16:47:00 +0200 Subject: [PATCH 013/992] added ictce easyconfig --- .../f/FDS/FDS-r18915-ictce-5.5.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb new file mode 100644 index 0000000000..ef3f6f0041 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb @@ -0,0 +1,24 @@ +name = 'FDS' +version = 'r18915' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """ + Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and + heat transport from fires. +""" +toolchain = {'name': 'ictce', 'version': '5.5.0'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +patches = ['FDS_makefile.patch'] +modextrapaths = {'PATH': 'FDS_Source'} + +sanity_check_paths = { + 'files': ['FDS_Source/fds'], + 'dirs': [], +} +moduleclass = 'phys' -- GitLab From 0d7fbaff77990066bd537a1ada4fa77fa96bd838 Mon Sep 17 00:00:00 2001 From: Andreas Panteli Date: Fri, 11 Apr 2014 12:16:01 +0300 Subject: [PATCH 014/992] Contribute Perl module Parallel-ForkManager --- ...rkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..b35839d741 --- /dev/null +++ b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli +# License:: MIT/GPL +# +## + +easyblock = 'PerlModule' + +name = 'Parallel-ForkManager' +version = '1.06' + +homepage = 'http://search.cpan.org/~szabgab/Parallel-ForkManager-1.06/lib/Parallel/ForkManager.pm' +description = """A simple parallel processing fork manager""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://search.cpan.org/CPAN/authors/id/S/SZ/SZABGAB/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver) +] + +options = {'modulename': 'Parallel::ForkManager'} + +moduleclass = 'data' -- GitLab From 82ad16ec61eda751ad121612655afb7d8ca85319 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 14 Apr 2014 19:25:24 +0200 Subject: [PATCH 015/992] IMPUTE2 2.3.0 easyconfigs --- .../i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb | 32 +++++++++++++++++++ .../i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb create mode 100644 easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb new file mode 100644 index 0000000000..0c2d1cc059 --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'IMPUTE2' +version = '2.3.0' +versionsuffix = '_x86_64_dynamic' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb new file mode 100644 index 0000000000..0fb795f7eb --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'IMPUTE2' +version = '2.3.0' +versionsuffix = '_x86_64_static' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + -- GitLab From 13a31a1ba2f7b3ce9b3593d85af03f450a1363a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Apr 2014 09:18:08 +0200 Subject: [PATCH 016/992] add easyconfig files for IMa2 --- .../i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb | 23 +++++++++++++++++++ .../i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100755 easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb create mode 100755 easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb new file mode 100755 index 0000000000..690d220498 --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'IMa2' +version = '8.27.12' + +homepage = 'https://bio.cst.temple.edu/~hey/software/software.htm#IMa2' +description = """IMa2 is a progam for population genetic analysis that can handle two or more populations.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://bio.cst.temple.edu/~hey/program_files/IMa2'] +sources = [SOURCELOWER_TAR_GZ] + +with_configure = True + +files_to_copy = [(['src/IMa2'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/IMa2"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb new file mode 100755 index 0000000000..a3ed62f5d6 --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'IMa2' +version = '8.27.12' + +homepage = 'https://bio.cst.temple.edu/~hey/software/software.htm#IMa2' +description = """IMa2 is a progam for population genetic analysis that can handle two or more populations.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://bio.cst.temple.edu/~hey/program_files/IMa2'] +sources = [SOURCELOWER_TAR_GZ] + +with_configure = True + +files_to_copy = [(['src/IMa2'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/IMa2"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6af8de3001d1c136b9f5456ce61399f30a81284e Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 19 May 2014 14:07:41 +0200 Subject: [PATCH 017/992] CUDA-6.0.37.eb --- easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb | 29 +++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb new file mode 100644 index 0000000000..f6e34de664 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +name = 'CUDA' +version = '6.0.37' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. http://developer.download.nvidia.com/compute/cuda/5_0/rel-update-1/installers/cuda_5.0.35_linux_64_rhel5.x-1.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_0/rel/installers/'] + +sources = ['%(namelower)s_%(version)s_linux_64.run'] + +moduleclass = 'system' -- GitLab From 47b95ac76e0393c0c7bb47ad786e8e62dda7d1e3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 19 May 2014 14:20:43 +0200 Subject: [PATCH 018/992] added %(version_minor)s to source_urls updated the download url example --- easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb index f6e34de664..0ebf372eeb 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -21,9 +21,8 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'dummy', 'version': 'dummy'} -# eg. http://developer.download.nvidia.com/compute/cuda/5_0/rel-update-1/installers/cuda_5.0.35_linux_64_rhel5.x-1.run -source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_0/rel/installers/'] - +# http://developer.download.nvidia.com/compute/cuda/6_0/rel/installers/cuda_6.0.37_linux_64.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/rel/installers/'] sources = ['%(namelower)s_%(version)s_linux_64.run'] moduleclass = 'system' -- GitLab From 1078dea61a9a624e1907bb7eb7b6a78c3b0e609d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Jun 2014 16:13:41 +0200 Subject: [PATCH 019/992] add easyconfig for ADF --- .../a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100755 easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb diff --git a/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb new file mode 100755 index 0000000000..6395f17b38 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = "ADF" +version = '2009.01a.pc64_linux.intelmpi' + +homepage = 'http://www.scm.com/' +description = "ADF is a premium-quality quantum chemistry software package based on Density Functional Theory (DFT)." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s%(version)s.bin.tgz'] + +dependencies = [('impi', '3.2.2.006')] + +sanity_check_paths = { + 'files': ['bin/adf', 'bin/adf.exe'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 20f4e3e6279fe5d8de7f4ebc87b77d16944155cf Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Fri, 4 Jul 2014 16:10:41 +1200 Subject: [PATCH 020/992] new toolchain release added --- .../easyconfigs/i/imkl/imkl-10.3.12.361.eb | 8 ++-- .../easyconfigs/i/impi/impi-4.1.0.027.eb | 2 +- easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb | 23 +++++++++++ easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb | 23 +++++++++++ .../OpenMPI-1.6.5-iccifort-2011.13.367.eb | 38 ++++++++++++++++++ .../OpenMPI-1.6.5-iccifort-2013.4.183.eb | 39 +++++++++++++++++++ 6 files changed, 127 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index 0db4c8f64f..dfb97e3568 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -9,14 +9,12 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_mkl_%(version)s.tgz'] - -compver = '2011.13.367' +sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] # deps for interface build dependencies = [ - ('icc', compver), - ('ifort', compver), + ('icc', '2011.13.367'), + ('ifort', '2011.13.367'), ('impi', '4.1.0.027'), ] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 839fe8f604..d074eeb0ea 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_mpi_p_%(version)s.tgz'] +sources = ['/share/src/Intel/2011/l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb b/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb new file mode 100644 index 0000000000..6a4ff077e3 --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '6.5.4' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2013.4.183' +comp = ('iccifort', compver) +ompi = 'OpenMPI' +ompiver = '1.6.5' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + (ompi, ompiver, '', comp), + ('imkl', '11.0.4.183', '-%s-%s' % (ompi, ompiver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb b/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb new file mode 100644 index 0000000000..1d73c1141d --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '6.7.2' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2013.4.183' +comp = ('iccifort', compver) +ompi = 'OpenMPI' +ompiver = '1.6.5' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + (ompi, ompiver, '', comp), + ('imkl', '11.1.2.144', '-%s-%s' % (ompi, ompiver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb new file mode 100644 index 0000000000..17ecb57b0f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb @@ -0,0 +1,38 @@ +name = 'OpenMPI' +version = '1.6.5' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2011.13.367'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support + +dependencies = [('hwloc', '1.6')] + +# needed for --with-openib +if OS_NAME in ['debian', 'ubuntu']: + osdependencies = ['libibverbs-dev'] +else: + # OK for OS_NAME == redhat, fedora, RHEL, SL, centos + osdependencies = ['libibverbs-devel'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", + "mpi_f77", "mpi_f90", + "mpi", "ompitrace", "open-pal", + "otfaux", "otf", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", + "mpif-mpi-io", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb new file mode 100644 index 0000000000..29075bd3b2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb @@ -0,0 +1,39 @@ +name = 'OpenMPI' +version = '1.6.5' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2013.4.183'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib --with-pmi ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support + +dependencies = [('hwloc', '1.8.1')] + +# needed for --with-openib +if OS_NAME in ['debian', 'ubuntu']: + osdependencies = ['libibverbs-dev'] +else: + # OK for OS_NAME == redhat, fedora, RHEL, SL, centos + osdependencies = ['libibverbs-devel'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", + "mpi_f77", "mpi_f90", + "mpi", "ompitrace", "open-pal", + "otfaux", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", + "mpif-mpi-io", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From 7c463c7c7a9a2fdd69601fbc295a28a019059118 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 8 Jul 2014 21:02:33 +0200 Subject: [PATCH 021/992] cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb --- ...utadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..3a32415096 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.4.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0063db32993fb4a1c4418ce7019fad1d5d57b1f9 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 11:40:05 +0300 Subject: [PATCH 022/992] Adding ABINIT v.7.4.3 with dummy and goolf (parallel version) toolchains --- .../a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb | 38 +++++++++++++++++++ .../ABINIT-7.4.3-x86_64_linux_gnu4.5.eb | 32 ++++++++++++++++ .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 29 ++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb create mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..a3fe29c410 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'ABINIT' +version = '7.4.3' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://ftp.abinit.org/'] + +configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' + +dependencies = [ + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), +] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] + } + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb new file mode 100644 index 0000000000..fb4d81965f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +easyblock = "Tarball" + +name = 'ABINIT' +version = '7.4.3' +versionsuffix = '-x86_64_linux_gnu4.5' + +altversions = ['7.0.3', '7.0.4', '7.0.5'] + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 +sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] +source_urls = ['http://ftp.abinit.org/'] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] + } + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..350da2d908 --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'ETSF_IO' +version = '1.0.4' + +homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' +description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" + +dependencies = [ ('netCDF', '4.1.3') ] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] + } + +moduleclass = 'chem' -- GitLab From 38d072b44abb10c2bde6d7309c5a4466508f3040 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 11:45:37 +0300 Subject: [PATCH 023/992] Adding Bismark --- .../b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..d749578a18 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +easyblock = "Tarball" + +name = 'Bismark' +version = '0.10.1' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = """A tool to map bisulfite converted sequence reads and determine cytosine methylation states""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ["www.bioinformatics.babraham.ac.uk/projects/bismark/"] +sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] + + +dependencies = [ + ('Bowtie2', '2.0.2'), +] + +sanity_check_paths = { + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' -- GitLab From 845d1d8b8f8a44557e47d3220fb32db7cbba3162 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 12:38:12 +0300 Subject: [PATCH 024/992] Contributing DendroPy --- ...ndroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..d3ec591256 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,37 @@ +## +#This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = "PythonPackage" + +name = 'DendroPy' +version = '3.12.0' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. +""" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/D/DendroPy/'] +sources = ['%s-%s.tar.gz' % (name, version)] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +sanity_check_paths = { + 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py','bin/sumtrees.py','bin/strict_consensus_merge.py'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 34502fa5a0e9134260060cedb4af99061fa9c5d4 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 12:43:38 +0300 Subject: [PATCH 025/992] Contrib GATK v.3.0.0 --- .../g/GATK/GATK-3.0-0-Java-1.7.0_10.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb new file mode 100644 index 0000000000..13de380c1b --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '3.0-0' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] + +java = 'Java' +javaver = '1.7.0_10' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' -- GitLab From 7e3847fec5f46ecd5d41316da6410ae195213d3e Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 13:57:50 +0300 Subject: [PATCH 026/992] Contributing picard version 1.109 --- easybuild/easyconfigs/p/picard/picard-1.109.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-1.109.eb diff --git a/easybuild/easyconfigs/p/picard/picard-1.109.eb b/easybuild/easyconfigs/p/picard/picard-1.109.eb new file mode 100644 index 0000000000..b02c4dfde3 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-1.109.eb @@ -0,0 +1,14 @@ +name = 'picard' +version = '1.109' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.7.0_10')] + +moduleclass = 'bio' -- GitLab From a3ace75a4d542b028c8ba863fd3129f92f6ea5f7 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 13:59:59 +0300 Subject: [PATCH 027/992] Contrib Theano v.0.6.0 --- .../Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb | 30 ++++++++++++++++++ .../Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb | 31 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..8308ab148a --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.6.0' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions +involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ] + +sanity_check_paths = { + 'files': ['bin/theano-cache', + 'lib/python%s/site-packages/%s-%s-py%s.egg' % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] + } + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..1e72223824 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.6.0' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions + involving multi-dimensional arrays efficiently.""" + + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ] + +sanity_check_paths = { + 'files': ['bin/theano-cache', + 'lib/python%s/site-packages/%s-%s-py%s.egg' % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] + } + +moduleclass = 'math' -- GitLab From bd66b7e4bf46f52756c4199c803b5abab82f7a4e Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 14:09:32 +0300 Subject: [PATCH 028/992] Contributing MAT I/O Library --- .../m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..99d44c6862 --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'MATIO' +version = '1.5.2' + +homepage = 'http://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s-%s.zip' % (name.lower(), version)] + + +dependencies = [('zlib','1.2.7'), +] + +moduleclass = 'lib' -- GitLab From c2c5d304ff9411b2a303bd6e3e05a319a0e618ed Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 14:18:01 +0300 Subject: [PATCH 029/992] Contributing PROJ Cartographic Projections Library --- .../p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb | 26 +++++++++++++++++ .../p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 28 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..d3034c9b33 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'PROJ' +version = '4.8.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://download.osgeo.org/proj/'] + +sanity_check_paths = { + 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'dirs': [], + +} diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..618aab840c --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'PROJ' +version = '4.8.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://download.osgeo.org/proj/'] + +sanity_check_paths = { + 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'dirs': [], + +} + + -- GitLab From c76f17999c613ea2a5eb6647454d1d21bd3bc3d3 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 14:31:36 +0300 Subject: [PATCH 030/992] Contributing pBWA --- .../p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb new file mode 100644 index 0000000000..754be559e1 --- /dev/null +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = "MakeCp" + +name = 'pBWA' +version = '0.5.9_1.21009' + +homepage = 'http://pbwa.sourceforge.net/' +description = """pBWA is a parallel implementation of the popular software BWA. It was developed by modifying the BWA source code with the OpenMPI C library on the SHARCNET. pBWA has been successfully tested on other systems with the most basic OpenMPI installs. pBWA currently implements three commands from BWA: aln, samse, and sampe. pBWA retains and improves upon the multithreading provided by BWA while adding efficient parallelization for the above listed functions. pBWA has shown that its wall-time speedup is bounded only by the size of the parallel system available as pBWA can run on any number of nodes and/or cores simultaneously.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(name)s_%(version)s.zip'] +source_urls = [('http://sourceforge.net/projects/pbwa/files/latest', 'download')] + + + +dependencies = [ + ('BWA', '0.7.4'), +] + +files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] + +sanity_check_paths = { + 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], + 'dirs': ['.'], + +} + +moduleclass = 'bio' -- GitLab From 5c525705338558ca807cb3a8cab284a02f714309 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Thu, 7 Aug 2014 14:49:43 +0300 Subject: [PATCH 031/992] Minor changes to config files --- .../easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb | 8 ++++---- easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 10 ++++------ 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb index d3034c9b33..52eec6cca7 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -11,7 +11,8 @@ name = 'PROJ' version = '4.8.0' homepage = 'http://trac.osgeo.org/proj/' -description = """Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates""" +description = """Program proj is a standard Unix filter function which converts + geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -20,7 +21,6 @@ sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://download.osgeo.org/proj/'] sanity_check_paths = { - 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], - 'dirs': [], - + 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'dirs': [], } diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb index 618aab840c..f62a689830 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -11,7 +11,8 @@ name = 'PROJ' version = '4.8.0' homepage = 'http://trac.osgeo.org/proj/' -description = """Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates""" +description = """Program proj is a standard Unix filter function which converts + geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -20,9 +21,6 @@ sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://download.osgeo.org/proj/'] sanity_check_paths = { - 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], - 'dirs': [], - + 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'dirs': [], } - - -- GitLab From 3c3004285127ac62d3e5b2158b6834739a930a40 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Thu, 7 Aug 2014 15:04:45 +0300 Subject: [PATCH 032/992] A few more changes --- easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb index 52eec6cca7..4661417502 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -17,8 +17,8 @@ description = """Program proj is a standard Unix filter function which converts toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} -sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb index f62a689830..589656723f 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -17,8 +17,8 @@ description = """Program proj is a standard Unix filter function which converts toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} -sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], -- GitLab From 12de7b508c63a9ee2395608700c534cc3bd8edc1 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Thu, 14 Aug 2014 15:30:05 +1200 Subject: [PATCH 033/992] Score-P goolf-1.5.14 --- .../c/Cube/Cube-4.2.3-goolf-1.5.14.eb | 35 +++++++++++++++ .../o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb | 26 +++++++++++ .../p/PDT/PDT-3.20-goolf-1.5.14.eb | 45 +++++++++++++++++++ .../s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb | 39 ++++++++++++++++ 4 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb new file mode 100644 index 0000000000..8bc6ecb55a --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## +easyblock = 'EB_Score_minus_P' + +name = "Cube" +version = "4.2.3" + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist'] + +patches = ['Cube-4.2_fix-Qt-version-check.patch'] + +dependencies = [('Qt', '4.8.4')] + +configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" + +sanity_check_paths = { + 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb new file mode 100644 index 0000000000..c2bd8f4970 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -0,0 +1,26 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## +name = "OPARI2" +version = "1.1.2" + +homepage = 'http://www.score-p.org' +description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, + is a source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls to + the POMP2 measurement interface.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +sanity_check_paths = { + 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb new file mode 100644 index 0000000000..1933e4066b --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb @@ -0,0 +1,45 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## +name = "PDT" +version = "3.20" + +homepage = 'http://www.cs.uoregon.edu/research/pdt/' +description = """Program Database Toolkit (PDT) is a framework for analyzing source + code written in several programming languages and for making rich program knowledge + accessible to developers of static and dynamic analysis tools. PDT implements a standard + program representation, the program database (PDB), that can be accessed in a uniform way + through a class library supporting common PDB operations.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +prefix_opt = '-prefix=' + +# notes by Bernd Mohr +# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect +# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc +configopts = '-GNU' + +keeppreviousinstall = True + +# notes by Bernd Mohr +# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? +sanity_check_paths = { + 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], + 'dirs': [], +} + +skipsteps = ['build'] + +modextrapaths = { + 'PATH': "x86_64/bin", + 'LD_LIBRARY_PATH': "x86_64/lib", +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb new file mode 100644 index 0000000000..196dc0e191 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +# make sure we don't fall back to the ConfigureMake easyblock +easyblock = 'EB_Score_minus_P' + +name = "Score-P" +version = "1.2.3" + +homepage = 'http://www.score-p.org' +description = """The Score-P measurement infrastructure is a highly scalable and + easy-to-use tool suite for profiling, event tracing, and online analysis of HPC + applications.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {"usempi": True} + +# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz +sources = ["scorep-%(version)s.tar.gz"] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.22'), + ('Cube', '4.2.3'), + ('OPARI2', '1.1.2'), + ('OTF2', '1.2.1'), + ('PAPI', '5.2.0'), + ('PDT', '3.20'), +] + +sanity_check_paths = { + 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", + ("lib64/libscorep_adapter_mpi_event.a", "lib/libscorep_adapter_mpi_event.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 659dca6f9820e2e88f218586eaf1cf1687788377 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Thu, 14 Aug 2014 16:59:41 +1200 Subject: [PATCH 034/992] missing dependencies --- .../b/binutils/binutils-2.22-goolf-1.5.14.eb | 33 ++++++++++++++ .../o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb | 31 +++++++++++++ .../p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb | 44 +++++++++++++++++++ .../easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb | 17 +++++++ 4 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb new file mode 100644 index 0000000000..e4a2454e0e --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +name = 'binutils' +version = '2.22' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils-2.22: GNU binary utilities" + +sources = ['binutils-%s.tar.bz2' % version] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'pic': True} + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..e0a03c63d3 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'EB_Score_minus_P' + +name = "OTF2" +version = "1.2.1" + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It will become the new standard trace format + for Scalasca, Vampir, and Tau and is open for other tools.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +sanity_check_paths = { + # note by Bernd Mohr: on some systems libraries end up in lib/ + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..f1dcf6fbfe --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +name = 'PAPI' +version = '5.2.0' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# Example download URL, for reference: http://icl.cs.utk.edu/projects/papi/downloads/papi-5.0.0.tar.gz +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb new file mode 100644 index 0000000000..e0d6a9d420 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb @@ -0,0 +1,17 @@ +name = 'Qt' +version = '4.8.4' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.34.3')] + +moduleclass = 'devel' -- GitLab From 84c026aa0326b20a09e0f53a6d7431b691369548 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Fri, 15 Aug 2014 15:41:43 +1200 Subject: [PATCH 035/992] minor changes --- easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb index 8bc6ecb55a..3628401ad4 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -21,8 +21,6 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist'] -patches = ['Cube-4.2_fix-Qt-version-check.patch'] - dependencies = [('Qt', '4.8.4')] configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" -- GitLab From 7f2076dcc517dcac3b51742cc86ddb20cc274adf Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:51:55 +1200 Subject: [PATCH 036/992] Delete imkl-10.3.12.361.eb --- .../easyconfigs/i/imkl/imkl-10.3.12.361.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb deleted file mode 100644 index dfb97e3568..0000000000 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ /dev/null @@ -1,29 +0,0 @@ -name = 'imkl' -version = '10.3.12.361' - -homepage = 'http://software.intel.com/en-us/intel-mkl/' -description = """Intel Math Kernel Library is a library of highly optimized, - extensively threaded math routines for science, engineering, and financial - applications that require maximum performance. Core math functions include - BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] - -# deps for interface build -dependencies = [ - ('icc', '2011.13.367'), - ('ifort', '2011.13.367'), - ('impi', '4.1.0.027'), -] - -dontcreateinstalldir = 'True' - -interfaces = True - -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - -moduleclass = 'numlib' -- GitLab From 83ac4560b153fbadb3103c3cfb7b7efdb3691444 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:52:45 +1200 Subject: [PATCH 037/992] Delete impi-4.1.0.027.eb --- .../easyconfigs/i/impi/impi-4.1.0.027.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb deleted file mode 100644 index d074eeb0ea..0000000000 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'impi' -version = '4.1.0.027' - -homepage = 'http://software.intel.com/en-us/intel-mpi-library/' -description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message - passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['/share/src/Intel/2011/l_mpi_p_%(version)s.tgz'] - -dontcreateinstalldir = 'True' - -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - -moduleclass = 'mpi' -- GitLab From 2cd359ce10c48b88098b66a755b91b9b0f5e9f92 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:53:23 +1200 Subject: [PATCH 038/992] Delete iomkl-6.5.4.eb --- easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb | 23 -------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb b/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb deleted file mode 100644 index 6a4ff077e3..0000000000 --- a/easybuild/easyconfigs/i/iomkl/iomkl-6.5.4.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = "Toolchain" - -name = 'iomkl' -version = '6.5.4' - -homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -compver = '2013.4.183' -comp = ('iccifort', compver) -ompi = 'OpenMPI' -ompiver = '1.6.5' - -dependencies = [ - ('icc', compver), - ('ifort', compver), - (ompi, ompiver, '', comp), - ('imkl', '11.0.4.183', '-%s-%s' % (ompi, ompiver)), -] - -moduleclass = 'toolchain' -- GitLab From 18d8c907244260a2ee1c496ad781e1bb7b49e5ee Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:53:35 +1200 Subject: [PATCH 039/992] Delete iomkl-6.7.2.eb --- easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb | 23 -------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb b/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb deleted file mode 100644 index 1d73c1141d..0000000000 --- a/easybuild/easyconfigs/i/iomkl/iomkl-6.7.2.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = "Toolchain" - -name = 'iomkl' -version = '6.7.2' - -homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -compver = '2013.4.183' -comp = ('iccifort', compver) -ompi = 'OpenMPI' -ompiver = '1.6.5' - -dependencies = [ - ('icc', compver), - ('ifort', compver), - (ompi, ompiver, '', comp), - ('imkl', '11.1.2.144', '-%s-%s' % (ompi, ompiver)), -] - -moduleclass = 'toolchain' -- GitLab From ad4b011978294898c2df6b06b3a3136f4f449e51 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:54:41 +1200 Subject: [PATCH 040/992] Delete OpenMPI-1.6.5-iccifort-2011.13.367.eb --- .../OpenMPI-1.6.5-iccifort-2011.13.367.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb deleted file mode 100644 index 17ecb57b0f..0000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2011.13.367.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'OpenMPI' -version = '1.6.5' - -homepage = 'http://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-2 implementation.""" - -toolchain = {'name': 'iccifort', 'version': '2011.13.367'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' -configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support - -dependencies = [('hwloc', '1.6')] - -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] - -sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", "otf", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + - ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", - "mpif-mpi-io", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], -} - -moduleclass = 'mpi' -- GitLab From 75ea4b4daf3d4a3556766f4a8dac11f9dd519cb6 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 15 Aug 2014 15:54:57 +1200 Subject: [PATCH 041/992] Delete OpenMPI-1.6.5-iccifort-2013.4.183.eb --- .../OpenMPI-1.6.5-iccifort-2013.4.183.eb | 39 ------------------- 1 file changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb deleted file mode 100644 index 29075bd3b2..0000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013.4.183.eb +++ /dev/null @@ -1,39 +0,0 @@ -name = 'OpenMPI' -version = '1.6.5' - -homepage = 'http://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-2 implementation.""" - -toolchain = {'name': 'iccifort', 'version': '2013.4.183'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib --with-pmi ' -configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support - -dependencies = [('hwloc', '1.8.1')] - -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] - -sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + - ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", - "mpif-mpi-io", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], -} - -moduleclass = 'mpi' -- GitLab From fec5c07c530a026d72130cac630ff7c57868c4ce Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Fri, 15 Aug 2014 16:00:57 +1200 Subject: [PATCH 042/992] minor change --- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index dfb97e3568..9b7df526e4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] +sources = ['l_mkl_%(version)s_intel64.tgz'] # deps for interface build dependencies = [ -- GitLab From f11a48a7040e02bbb5a7ab04f139f143636cd3e7 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Aug 2014 13:46:16 +0200 Subject: [PATCH 043/992] added new cutadapt for intel --- .../cutadapt-1.5-intel2014b-Python-2.7.8.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..9be9435a32 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.5' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://pypi.python.org/packages/source/c/cutadapt/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 8b475b5b932795cbdf9d4fd509bbbbf075635bd6 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 23 Aug 2014 22:26:06 +0200 Subject: [PATCH 044/992] STAR goolf-1.4.10 --- .../s/STAR/STAR-2.3.0e-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../s/STAR/STAR_missing_includes.patch | 10 ++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb new file mode 100644 index 0000000000..aaedf45292 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.3.0e' + +homepage = 'https://code.google.com/p/rna-star/' +description = """ STAR aligns RNA-seq reads to a reference genome using + uncompressed suffix arrays. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://rna-star.googlecode.com/files/'] +sources = ['%(name)s_%(version)s.tgz'] + +patches = ['STAR_missing_includes.patch'] + +# a binary is provided with the source files. We delete it +premakeopts = 'rm STAR && ' + +parallel = 1 + +files_to_copy = [(["STAR"], "bin"), "README.txt"] + +sanity_check_paths = { + 'files': ["bin/STAR"], + 'dirs': [""], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch b/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch new file mode 100644 index 0000000000..82d8f2d8e0 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch @@ -0,0 +1,10 @@ +--- STAR_2.3.0e.orig/Genome.cpp 2013-01-22 21:51:14.000000000 +0100 ++++ STAR_2.3.0e/Genome.cpp 2014-08-23 22:06:02.954503545 +0200 +@@ -6,6 +6,7 @@ + #include "streamFuns.h" + #include + #include ++#include + + #define SHM_sizeG 0 + #define SHM_sizeSA 8 -- GitLab From 30ebeb7abc101c84a786e4eeec51b65cc80065db Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 24 Aug 2014 13:53:43 +0200 Subject: [PATCH 045/992] IDBA-UD-1.1.1-goolf-1.4.10.eb --- .../i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..43d9e4ed11 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in premakeopts +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.1' + +homepage = 'http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads + Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. + IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth + contigs are removed iteratively with cutoff threshold from low to high to reduce the errors + in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled + locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD + can iterate k value of de Bruijn graph to a very large value with less gaps and less branches + to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://hku-idba.googlecode.com/files/'] +sources = ['idba-%(version)s.tar.gz'] + +premakeopts = './configure && ' + +# we delete every .o file which is left in bin folder +makeopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' + +files_to_copy = ["bin", "script", "README", "ChangeLog", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' + -- GitLab From 30e0006a8e2c9f614bdfec4d2c2b8e3b3b28a4cd Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Sep 2014 18:19:13 +0200 Subject: [PATCH 046/992] added tabbix easyonfigs --- .../t/tabix/tabix-0.2.6-goolf-1.4.10.eb | 36 +++++++++++++++++++ .../t/tabix/tabix-0.2.6-intel-2014b.eb | 30 ++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb new file mode 100644 index 0000000000..175efc7a74 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock='MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] +makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb new file mode 100644 index 0000000000..2f4bddea4e --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -0,0 +1,30 @@ +easyblock='MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] +makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' -- GitLab From 97176bfc0696547a7a6314bf0a66c41e075c77b7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Sep 2014 10:39:30 +0200 Subject: [PATCH 047/992] PostgreSQL with Perl binding --- .../DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 26 ++++++++++++ .../PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb | 41 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000..5caf1511aa --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'DBD-Pg' +version = '3.4.1' + +homepage = 'http://search.cpan.org/~turnstep/DBD-Pg-3.4.1/' +description = """Perl binding for PostgreSQL""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TU/TURNSTEP/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("PostgreSQL", "9.3.5"), +] + + +options = {'modulename': 'DBD::Pg'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb new file mode 100644 index 0000000000..9b40199a4f --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb @@ -0,0 +1,41 @@ +name = 'PostgreSQL' +version = '9.3.5' + +homepage = 'http://www.mysql.com/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2014b'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +java = 'Java' +javaver = '1.7.0_60' + +dependencies = [ + (java, javaver, '', True), + ('libreadline', '6.3'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), + ('Perl', '5.20.0'), +] + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 36aa12e557164986ff49d4fced15e9c03dd44d09 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Sep 2014 14:27:46 +0200 Subject: [PATCH 048/992] Typo Corrected --- ...geSQL-9.3.5-intel-2014b.eb => PostgreSQL-9.3.5-intel-2014b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PostgreSQL/{PostgeSQL-9.3.5-intel-2014b.eb => PostgreSQL-9.3.5-intel-2014b.eb} (100%) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb rename to easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb -- GitLab From 0943e87b0ea092d881f2b7e5d7bc6cfa15cde0f1 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 8 Sep 2014 12:49:29 +0200 Subject: [PATCH 049/992] updated download urls --- .../b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb | 4 ++-- .../b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb | 4 ++-- .../b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb index e0f3e3aa78..e3bd679270 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.','-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb index 772e359455..d030d9efdd 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.','-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb index 644fe3ba68..f1be6ce30a 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.','-')] perl = 'Perl' perlver = '5.16.3' -- GitLab From e7c3b62cd358037b8d85cd6d4a3ced20c84540d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Fri, 12 Sep 2014 10:08:24 +0200 Subject: [PATCH 050/992] Update DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb --- .../d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index 5caf1511aa..8e07224960 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -15,10 +15,7 @@ perl = 'Perl' perlver = '5.20.0' versionsuffix = '-%s-%s' % (perl, perlver) -dependencies = [ - (perl, perlver), - ("PostgreSQL", "9.3.5"), -] +dependencies = [(perl, perlver), ("PostgreSQL", "9.3.5")] options = {'modulename': 'DBD::Pg'} -- GitLab From c62fc4a88b50b63e1461f8b02a5d045b31cdf85a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Fri, 12 Sep 2014 10:08:34 +0200 Subject: [PATCH 051/992] Update DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb --- .../easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index 8e07224960..ca812f75ef 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -17,7 +17,6 @@ versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [(perl, perlver), ("PostgreSQL", "9.3.5")] - options = {'modulename': 'DBD::Pg'} moduleclass = 'data' -- GitLab From d0e3c5a86c5e372ac14c4d2a4f54aa22e7ad02a4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 16 Sep 2014 10:40:06 +0200 Subject: [PATCH 052/992] CUDA 6.5.14 --- easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb | 29 +++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb new file mode 100644 index 0000000000..2698ca5e91 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +name = 'CUDA' +version = '6.5.14' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/'] + +sources = ['%(namelower)s_%(version)s_linux_64.run'] + +moduleclass = 'system' -- GitLab From 4ee9183cb074fa0e245949a0c797c109057eaa9f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 22 Sep 2014 17:43:17 +0200 Subject: [PATCH 053/992] added tecplot easyconfig --- .../t/tecplot360ex/tecplot360ex.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb new file mode 100644 index 0000000000..08d437e5b8 --- /dev/null +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'tecplot360ex' +version = 'linux64' + +homepage = 'http://www.tecplot.com/' +description = """ + Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, + and communicate your results with professional images and animations. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://www.tecplot.com/my/product-releases/ +installername = '%(name)s_%(version)s.sh' +sources = [installername] + +sanity_check_paths = { + 'files': ['bin/tec360'], + 'dirs': [] +} +install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) +moduleclass = 'vis' + -- GitLab From a9ff525ef3cab6ff122bdc52f66e57bd3755efcb Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 6 Oct 2014 17:07:43 +0200 Subject: [PATCH 054/992] added ngsipce --- .../n/ngspice/ngspice-26-intel-2014b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb new file mode 100644 index 0000000000..371953f64b --- /dev/null +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -0,0 +1,26 @@ +name = 'ngspice' +version = '26' + +homepage = 'http://ngspice.sourceforge.net' +description = """Ngspice is a mixed-level/mixed-signal circuit simulator. Its code + is based on three open source software packages: Spice3f5, Cider1b1 + and Xspice. +""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = { + ('Bison', '3.0.2'), + ('flex', '2.5.39'), +} +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ngmakeidx', 'ngmultidec', 'ngnutmeg', 'ngproc2mod', 'ngsconvert', 'ngspice']], + 'dirs': [], +} + + +moduleclass = 'lang' -- GitLab From 50debd2f2efd461b7970065d9fe5b68a19b69b1a Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 6 Oct 2014 17:10:50 +0200 Subject: [PATCH 055/992] set correct moduleclass --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index 371953f64b..ca40da2a30 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -23,4 +23,4 @@ sanity_check_paths = { } -moduleclass = 'lang' +moduleclass = 'cae' -- GitLab From 38fc2d5668853b38041f8cc00d30cbca19efcddb Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 6 Oct 2014 17:12:41 +0200 Subject: [PATCH 056/992] remove whitespace --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index ca40da2a30..baa9131dc8 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -22,5 +22,4 @@ sanity_check_paths = { 'dirs': [], } - moduleclass = 'cae' -- GitLab From 381b0341849d633c556c066b9e83fabf8843fc02 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 6 Oct 2014 17:43:10 +0200 Subject: [PATCH 057/992] be compatible with python 2.7.4 and lower --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index baa9131dc8..16f1a1e3ae 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -13,10 +13,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = { +dependencies = [ ('Bison', '3.0.2'), ('flex', '2.5.39'), -} +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ngmakeidx', 'ngmultidec', 'ngnutmeg', 'ngproc2mod', 'ngsconvert', 'ngspice']], 'dirs': [], -- GitLab From f5e3d801b8d5854f755b21bd133cf92099e606af Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 9 Oct 2014 15:01:07 +0200 Subject: [PATCH 058/992] Pindel-0.2.5a7-goolf-1.4.10.eb --- .../p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb new file mode 100644 index 0000000000..40569a3495 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'CmdCp' + +name = 'Pindel' +version = '0.2.5a7' + +homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' +description = """ Pindel can detect breakpoints of large deletions, medium sized +insertions, inversions, tandem duplications and other structural variants at single-based +resolution from next-gen sequence data. It uses a pattern growth approach to identify the +breakpoints of these variants from paired-end short reads. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/genome/pindel/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('SAMtools', '0.1.19')] + +cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] + +files_to_copy = [(['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), + "demo", "gmt", "gmt-web", "test", "README.md", "RELEASE" + ] + +postinstallcmds = ["sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bam2pindel.pl"] + +sanity_check_paths = { + 'files': ['bin/pindel', 'bin/sam2pindel', 'bin/pindel2vcf', 'bin/bam2pindel.pl'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c3c5b253a04ac10193c861fc7dcdbe8c6e2876cf Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 9 Oct 2014 17:29:23 +0200 Subject: [PATCH 059/992] indent description --- .../easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 40569a3495..f573781fab 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -10,9 +10,9 @@ version = '0.2.5a7' homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' description = """ Pindel can detect breakpoints of large deletions, medium sized -insertions, inversions, tandem duplications and other structural variants at single-based -resolution from next-gen sequence data. It uses a pattern growth approach to identify the -breakpoints of these variants from paired-end short reads. """ + insertions, inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data. It uses a pattern growth approach to identify the + breakpoints of these variants from paired-end short reads. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} -- GitLab From f9e11c7393bfbf54d69dceae4a80d7987a71268c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 17:56:05 +0200 Subject: [PATCH 060/992] add easyconfig for WIEN2k v14.1 with intel/2014b --- .../w/WIEN2k/WIEN2k-14.1-intel-2014b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb new file mode 100644 index 0000000000..9a8f71d9ca --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb @@ -0,0 +1,46 @@ +name = 'WIEN2k' +version = '14.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['b926596ea86d505120af8829cec4814e'] + +patches = [ + 'WIEN2k-%(version)s_lapw5-main-accuracy-fix.patch', + 'WIEN2k-%(version)s_fix-tetra.patch', + 'WIEN2k-%(version)s_fix-x_lapw.patch', +] + +dependencies = [('FFTW', '3.3.4')] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), +] + +moduleclass = 'chem' -- GitLab From b9c43dfe98cf7377649301ad3a894beae3a99213 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:29:47 +0200 Subject: [PATCH 061/992] add missing patch files for WIEN2k 14.1 --- .../w/WIEN2k/WIEN2k-14.1_fix-tetra.patch | 57 +++ .../w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch | 461 ++++++++++++++++++ .../WIEN2k-14.1_lapw5-main-accuracy-fix.patch | 22 + 3 files changed, 540 insertions(+) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch new file mode 100644 index 0000000000..ef8bc83ba2 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch @@ -0,0 +1,57 @@ +see http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11178.html +--- WIEN2k_14.orig/SRC_tetra/tetra.f 2014-09-19 13:30:20.757390463 +0200 ++++ WIEN2k_14/SRC_tetra/tetra.f 2014-09-19 13:30:37.671774186 +0200 +@@ -165,7 +165,7 @@ + SO=1.d0 + NSORT=1 + KLMAX=1 +- allocate( TEXT(Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) ++ allocate( TEXT(0:Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) + IDOS(1,1)=0 + IDOS(1,2)=0 + DOSTYP(1)='TOTAL' +@@ -220,7 +220,7 @@ + READ(4,1010) ALAT1,ALAT2,ALAT3,EFERM + READ(4,1020) MINWAV,MAXWAV,KSPIN,NSORT,kso,kLmax + if(klmax.eq.0) klmax=14 +- allocate( TEXT(Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) ++ allocate( TEXT(0:Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) + ! INCREASE NSORT BY ONE FOR THE INTERSTITIAL DOS (OUT) + NSORT=NSORT+1 + WRITE(6,2000) SYSTEM +@@ -240,7 +240,7 @@ + DO 107 ISORT=1,NSORT + IF(ISORT.EQ.NSORT) GOTO 107 + READ(4,1030) JATOM,NEQU,isplit,text(isort) +- WRITE(6,2030) JATOM,NEQU,isplit,text(isort) ++ WRITE(6,2030) JATOM,NEQU,isplit,text(isort) + 107 CONTINUE + nndos_save=nndos + DO 90 JCASE=1,NNDOS +@@ -364,7 +364,11 @@ + if(nst.eq.1.and.ibrsw.eq.-1) then ! for one k-point calculate the DOS with broadening + ibrsw=1 + print*,'Only 1 k-point, switching to Gauss-broadening with',br +- endif ++ if(br.lt.1.d-6) then ++ br=0.002 ++ print*,' No broadening specified, increasing broadening to',br ++ endif ++ endif + if(ibrsw.ne.-1) then + CALL broadDOS (ibrsw,br,brlor,NNDOS,1,JEND,EMIN,EMAX,NYMIN,NYMAX,DE,ebs,fc,nst,densty) + endif +@@ -523,7 +527,7 @@ + 1000 FORMAT(1X,A70,/) + 1010 FORMAT(1X,15X,3F8.5,16X,F10.5) + 1020 FORMAT(1X,I4,10X,I4,8X,I1,7X,I3,8x,i2,6x,i3) +- 1030 FORMAT(6X,I3,7X,I2,9x,i2,2x,a200) ++ 1030 FORMAT(6X,I3,7X,I2,9x,i2,2x,a96) + 1040 FORMAT(6X,I4) + 1041 FORMAT(5X,I5) + 1050 FORMAT(F10.5,I3,F8.5,3X,(40F8.5)) +@@ -532,3 +536,4 @@ + 2020 FORMAT(1X,I4,' < NMAT < ',I4,3X,'SPIN=',I1,3X,'NATO=',I4) + 2030 FORMAT(1X,'JATOM',I3,2X,'MULT=',I2,2x,'ISPLIT=',i2,2x,a96) + END ++ diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch new file mode 100644 index 0000000000..a17c8dbe58 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch @@ -0,0 +1,461 @@ +see http://zeus.theochem.tuwien.ac.at/pipermail/wien/2014-September/021667.html +--- x_lapw.orig 2014-10-09 15:03:02.181799391 +0200 ++++ x_lapw 2014-10-09 15:08:25.254125143 +0200 +@@ -4,28 +4,28 @@ + set running = ".running.$$.`hostname`.`date +%d%m%H%M%S`" + echo $$ >$running + onintr clear +-alias error 'echo ">>> ($name) \!* -> exit"; goto error' ++alias error 'echo ">>> ($name) \!* -> exit"; goto error' + +-set name = $0 #full name of script-file +-set bin = $name:h #default directory for WIEN-executables ++set name = $0 #full name of script-file ++set bin = $name:h #default directory for WIEN-executables + if !(-d $bin) set bin = . +-set name = $name:t ++set name = $name:t + +-set def = def #def-file +-set tmp = ( ) #tmp-files, to be deleted before exit +-set log = :log #log-file +-set t = time # +-set updn # spinpolarization switch +-set dnup = 'dn' # spinpolarization switch ++set def = def #def-file ++set tmp = ( ) #tmp-files, to be deleted before exit ++set log = :log #log-file ++set t = time # ++set updn # spinpolarization switch ++set dnup = 'dn' # spinpolarization switch + set spin=1 # for -it in lapw1 + #set ne_it=1.1 # for -it in lapw1 + set emin=-999.0 # for -emin XX in lapw2 + set emax=999.0 # for -all XX YY in lapw2 + set settol=0.00001 # tol parameter for sgroup + set wf=0 # wplot: WF to plot (0 = read from file) +-set sc # semicore-switch +-set so # spinorbit-switch +-set sodum # spinorbit-switch ++set sc # semicore-switch ++set so # spinorbit-switch ++set sodum # spinorbit-switch + #set cmplx + set cmplx1 + set cmplx2 +@@ -62,12 +62,12 @@ + unset efg # regular run in lapw2 + unset emin1 # regular run in lapw2 + unset emax1 # regular run in lapw2 +-unset command #command +-unset file #file-head +-unset deffile_only #create just def file +-unset fftstop #for dstart +-unset vresp #for lapw2 +-unset help_files #for lapw2 ++unset command #command ++unset file #file-head ++unset deffile_only #create just def file ++unset fftstop #for dstart ++unset vresp #for lapw2 ++unset help_files #for lapw2 + unset super # for dstart, creates new.clmsum + unset rxes # for tetra, uses rxes-weight file + unset rxesw # for tetra, writes rxes-weight file +@@ -88,9 +88,9 @@ + + if ( $?SCRATCH && $SCRATCH != '') then + set scratch=`echo $SCRATCH | sed -e 's/\/$//'`/ # we are afraid +- # different settings in different +- # computing centers +- #use global variable for scratch if set ++ # different settings in different ++ # computing centers ++ #use global variable for scratch if set + endif + set argv1=($argv) + +@@ -138,16 +138,16 @@ + shift; breaksw + case -it: + set iter +- shift; breaksw ++ shift; breaksw + case -noHinv: + set iter + unset readHinv +- shift; breaksw ++ shift; breaksw + case -noHinv0: + set iter + unset readHinv + set writeHinv +- shift; breaksw ++ shift; breaksw + # case -ne_it: + # shift;set ne_it=$1 + # shift; breaksw +@@ -169,36 +169,36 @@ + shift; breaksw + case -help_files: + set help_files +- shift; breaksw ++ shift; breaksw + case -vresp: + set vresp +- shift; breaksw ++ shift; breaksw + case -eece: + set eece=eece +- shift; breaksw ++ shift; breaksw + case -grr: + set grr=grr +- shift; breaksw ++ shift; breaksw + case -orb: + set orb +- shift; breaksw ++ shift; breaksw + case -nmat_only: + set nmat_only +- shift; breaksw ++ shift; breaksw + case -nohns: + set nohns +- shift; breaksw ++ shift; breaksw + case -enefile: + set enefile +- shift; breaksw ++ shift; breaksw + case -rxes: + set rxes +- shift; breaksw ++ shift; breaksw + case -rxesw: + set rxesw + shift;set rxese1 = $1 + shift;set rxese2 = $1 +- shift; breaksw ++ shift; breaksw + case -so: + set so = 'so' + set sodum = 'dum' +@@ -313,7 +313,7 @@ + endif + shift; breaksw + ## w2w stuff ## +- case -pp: # passed on to Wannier90 ++ case -pp: # passed on to Wannier90 + shift; breaksw + case -wf: + shift; set wf = $1 +@@ -338,7 +338,7 @@ + + if !($?file) then + set file = `pwd` +-set file = $file:t #tail of file-names ++set file = $file:t #tail of file-names + endif + + touch $file.struct +@@ -409,7 +409,7 @@ + #echo "`date`> ($name) $command $argv1[2-]" >> $log + echo "`date`> ($name) $argv1" >> $log + +-set def = $updn$command$sc.def ++set def = $updn$command$sc.def + #touch $def + + switch ($command) +@@ -1200,7 +1200,7 @@ + cat << theend > $def + 6,'$file.outputst', 'unknown','formatted' + 7,'$file.tmpden', 'unknown','formatted' +-10,'$file.tmp', 'unknown','unformatted' ++10,'$file.tmp', 'unknown','unformatted' + 11,'$file.vsp_st', 'unknown','formatted' + 12,'$file.vspdn_st', 'unknown','formatted' + 13,'$file.sigma', 'unknown','formatted' +@@ -1268,7 +1268,7 @@ + + case mixer_vresp: + set exe = mixer +- if !(-e $file.clmvalup || -z $file.clmvalup) then ++ if !(-e $file.clmvalup || -z $file.clmvalup) then + cat << theend > $def + 5,'$file.inm_vresp', 'old', 'formatted',0 + 6,'$file.outputm_vresp', 'unknown','formatted',0 +@@ -1283,7 +1283,7 @@ + 32,'$file.vrespbroyd2', 'unknown','unformatted',164896 + 51,'$file.vrespsum', 'unknown','formatted',0 + theend +- else ++ else + cat << theend > $def + 5,'$file.inm_vresp', 'old', 'formatted',0 + 6,'$file.outputm_vresp', 'unknown','formatted',0 +@@ -1304,7 +1304,7 @@ + 52,'$file.vrespdn', 'unknown','formatted',0 + 11,'$file.vrespsum', 'unknown','formatted',0 + theend +- endif ++ endif + breaksw + + +@@ -1318,7 +1318,7 @@ + cp $file.struct $file.struct_old + endif + set exe = $command +- if !(-e $file.clmvalup || -z $file.clmvalup) then ++ if !(-e $file.clmvalup || -z $file.clmvalup) then + cat << theend > $def + 5,'$file.inm', 'old', 'formatted',0 + 6,'$file.outputm', 'unknown','formatted',0 +@@ -1334,7 +1334,7 @@ + 32,'$file.broyd2', 'unknown','unformatted',164896 + 51,'$file.clmsum', 'unknown','formatted',0 + theend +- else ++ else + cat << theend > $def + 5,'$file.inm', 'old', 'formatted',0 + 6,'$file.outputm', 'unknown','formatted',0 +@@ -1364,7 +1364,7 @@ + echo "75,'$file.dmatdn_old','unknown','formatted',0" >> $def + echo "76,'$file.dmatud_old','unknown','formatted',0" >> $def + endif +- endif ++ endif + + if($eece == 'eece') then + echo "71,'$file.vorbup','unknown','formatted',0" >> $def +@@ -1557,16 +1557,16 @@ + if($para == para) then + set cnum=0 + if(-f .processes) then +- @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` +-# @ cnum+=1 ++ @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` ++# @ cnum+=1 + endif + #the original file will only be removed if there are sources to concat + if(-f "$file.output$typ$updnso" && $cnum>0) then +- rm "$file.output$typ$updnso" ++ rm "$file.output$typ$updnso" + endif + unset irr + if(-f "$file.irrep$hf$so${updn}_$cnum" && $cnum>0) then +- if(-f "$file.irrep$hf$so${updn}" ) rm "$file.irrep$hf$so${updn}" ++ if(-f "$file.irrep$hf$so${updn}" ) rm "$file.irrep$hf$so${updn}" + head -2 "$file.irrep$hf$so${updn}_$cnum" >"$file.irrep$hf$so${updn}" + set irr + endif +@@ -1574,9 +1574,9 @@ + while($count <= $cnum) + if($?irr) then + tail -n +3 $file.irrep$hf$so${updn}_$count >>$file.irrep$hf$so${updn} +- endif ++ endif + cat "$file.output$typ${updnso}_$count" >>"$file.output$typ$updnso" +- @ count++ ++ @ count++ + end + echo $file.output$typ$updnso created from $cnum parallel files + endif +@@ -2251,10 +2251,10 @@ + 7,'$file.amn$w90updn', 'unknown','formatted', 0 + 8,'$file.mmn$w90updn', 'unknown','formatted', 0 + 9,'${scratch}$file.vector$sc$hf$soupdn', 'unknown','unformatted',9000 +- 10,'$file.nnkp', 'old', 'formatted', 0 +- 12,'$file.eig$updn', 'unknown','formatted', 0 ++ 10,'$file.nnkp', 'old', 'formatted', 0 ++ 12,'$file.eig$updn', 'unknown','formatted', 0 + 18,'$file.vsp$updn', 'old', 'formatted', 0 +- 20,'$file.struct', 'old', 'formatted', 0 ++ 20,'$file.struct', 'old', 'formatted', 0 + 50,'$file.energy$soupdn', 'old', 'formatted', 0 + 51,'$file.fermi$updn' 'old', 'formatted', 0 + EOF +@@ -2296,23 +2296,23 @@ + if ($para == para) then + set cnum=0 + if(-f .processes) then +- @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` ++ @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` + endif + #the original file will only be removed if there are sources to concat + if(-f "$file.output$typ$updnso" && $cnum>0) then +- rm "$file.output$typ$updnso" ++ rm "$file.output$typ$updnso" + endif + set count=1 + while($count <= $cnum) + cat "$file.output$typ${updnso}_$count" >>"$file.output$typ$updnso" +- @ count++ ++ @ count++ + end + echo $file.output$typ$updnso created from $cnum parallel files + endif + cat >$def <$def + 4,'$file.klist', 'old', 'formatted', 0 + 10,'${scratch}$file.vector$sc$hf$so$updn', 'old', 'unformatted',0 +- 11,'$file.vector$sc$hf$so$updn', 'unknown','unformatted',0 +- 20,'$file.struct', 'old', 'formatted', 0 ++ 11,'$file.vector$sc$hf$so$updn', 'unknown','unformatted',0 ++ 20,'$file.struct', 'old', 'formatted', 0 + 50,'$file.energy$so$updn', 'old', 'formatted', 0 + 51,'$file.energy$so$updn', 'unknown','formatted', 0 + EOF +@@ -2402,7 +2402,7 @@ + ### end w2w ### + + default: +-error command $command does not exist ++error command $command does not exist + breaksw + + endsw +@@ -2445,10 +2445,11 @@ + if ($gw == 'gw') then + set exe = ($exe -gw) + endif +-endif ++endif + + echo $exe >>$running + $t $bin/$exe $def ++ + if($status != 0) then + echo "error: command $bin/$exe $def failed" + if ($?qtl || $?alm || $?almd || $?qdmft || $?band || $?fermi || $?efg || $?emin1 || $?emax1 ) then +@@ -2468,28 +2469,28 @@ + + set lapw2test=`echo $exe | cut -c 1-5` + if("$lapw2test" == 'lapw2') then ++ if ($?qtl || $?alm || $?almd || $?qdmft || $?band || $?fermi || $?efg || $?emin1 || $?emax1 ) then ++ if( -e .oldin2 ) mv .oldin2 $file.in2$cmplx ++ endif + if(! $?in1orig & ! $?band & ! $?emin1 & ! $?emax1) then +- if( -e $file.scf2$sc$updn && ! -z $file.scf2$sc$updn) then +- if($cmplx == 'c') then ++ if( -e $file.scf2$sc$updn && ! -z $file.scf2$sc$updn) then ++ if($cmplx == 'c') then + if(! (-e $file.in1$cmplx$sc && ! -z $file.in1$cmplx$sc)) set cmplx + endif +- set eferm=`grep ':FER :' $file.scf2$sc$updn|cut -f 2 -d=` +- set efold=`head -1 $file.in1$cmplx${sc}|cut -c11-17 | sed -e "s/[a-zA-Z(,=]//g"` ++ set eferm=`grep ':FER :' $file.scf2$sc$updn|cut -f 2 -d=` ++ set efold=`head -1 $file.in1$cmplx${sc}|cut -c11-17 | sed -e "s/[a-zA-Z(,=]//g"` + if($#efold == 0 ) set efold=0.5 +- set eferm=`echo " if($eferm > $efold) {if ($eferm > $efold + 0.2) {$efold + 0.2} else {$eferm} } else {if($eferm < $efold - 0.2) {$efold - 0.2} else ($eferm*0.75+$efold*0.25) }" | bc -l` # allow for max change of ef-old +- 0.2, pratt mix +- set modus=`head -1 $file.in1$cmplx${sc} | cut -c1-5` +- echo "$modus EF=$eferm (WFFIL, WFPRI, ENFIL, SUPWF) " >$file.in1$cmplx${sc}_tmp +- tail -n +2 $file.in1$cmplx${sc} >> $file.in1$cmplx${sc}_tmp +- mv $file.in1$cmplx${sc}_tmp $file.in1$cmplx${sc} +- endif ++ set eferm=`echo " if($eferm > $efold) {if ($eferm > $efold + 0.2) {$efold + 0.2} else {$eferm} } else {if($eferm < $efold - 0.2) {$efold - 0.2} else ($eferm*0.75+$efold*0.25) }" | bc -l` # allow for max change of ef-old +- 0.2, pratt mix ++ set modus=`head -1 $file.in1$cmplx${sc} | cut -c1-5` ++ echo "$modus EF=$eferm (WFFIL, WFPRI, ENFIL, SUPWF) " >$file.in1$cmplx${sc}_tmp ++ tail -n +2 $file.in1$cmplx${sc} >> $file.in1$cmplx${sc}_tmp ++ mv $file.in1$cmplx${sc}_tmp $file.in1$cmplx${sc} ++ endif + endif + endif + + clear: + #cleanup +-if ($?qtl || $?alm || $?almd || $?qdmft || $?band || $?fermi || $?efg || $?emin1 || $?emax1 ) then +- if( -e .oldin2 ) mv .oldin2 $file.in2$cmplx +-endif + if ($?rxesw ) then + if( -e .oldint ) mv .oldint $file.int + endif +@@ -2499,10 +2500,10 @@ + error: + rm $running + +-help: #help exit ++help: #help exit + cat << theend + +-USAGE: $0 PROGRAMNAME [flags] ++USAGE: $0 PROGRAMNAME [flags] + + PURPOSE:runs WIEN executables: afminput,aim,arrows,broadening,cif2struct, + clmaddsub,clmcopy,clminter,convham,conv2prim,dftd3,dipan,dmftproj, +@@ -2514,30 +2515,30 @@ + symmetso,telnes3,tetra,txspec,wannier90,w2w,w2waddsp,wplot,xspec + + FLAGS: +--f FILEHEAD -> FILEHEAD for path of struct & input-files +--t/-T -> suppress output of running time +--h/-H -> help +--d -> create only the def-file +--up -> runs up-spin +--dn -> runs dn-spin +--du -> runs up/dn-crossterm +--sc -> runs semicore calculation +--c -> complex calculation (no inversion symmetry present) ++-f FILEHEAD -> FILEHEAD for path of struct & input-files ++-t/-T -> suppress output of running time ++-h/-H -> help ++-d -> create only the def-file ++-up -> runs up-spin ++-dn -> runs dn-spin ++-du -> runs up/dn-crossterm ++-sc -> runs semicore calculation ++-c -> complex calculation (no inversion symmetry present) + -p -> run lapw0/1/2/hf/so/dm/optic in parallel (needs .machines or .processes file) + -scratch dir/ ->defines (and makes) $SCRATCH variable + -grr -> lapw0 for mBJ or hf (using $file.in0_grr) + -eece -> for hybrid-functionals (lapw0,lapw2,mixer,orb,sumpara) + -band -> for lapw1/2/hf bandstructures: uses *klist_band +--orb -> runs lapw1 with LDA+U/OP or B-ext correction, mixer with dmat +--it -> runs lapw1 with iterative diagonalization +--noHinv -> runs lapw1 with iterative diag. without Hinv +--noHinv0 -> runs lapw1 with iterative diag. writing new Hinv +--nohns -> runs lapw1 without HNS +--nmat_only-> runs lapw1 and yields only the matrixsize +--nmr -> runs lapw1 in NMR mode +--in1orig -> runs lapw2 but does not modify case.in1 +--emin X -> runs lapw2 with EMIN=X (in $file.in2$cmplx) +--all X Y -> runs lapw2 with ALL and E-window X-Y (in $file.in2$cmplx) ++-orb -> runs lapw1 with LDA+U/OP or B-ext correction, mixer with dmat ++-it -> runs lapw1 with iterative diagonalization ++-noHinv -> runs lapw1 with iterative diag. without Hinv ++-noHinv0 -> runs lapw1 with iterative diag. writing new Hinv ++-nohns -> runs lapw1 without HNS ++-nmat_only-> runs lapw1 and yields only the matrixsize ++-nmr -> runs lapw1 in NMR mode ++-in1orig -> runs lapw2 but does not modify case.in1 ++-emin X -> runs lapw2 with EMIN=X (in $file.in2$cmplx) ++-all X Y -> runs lapw2 with ALL and E-window X-Y (in $file.in2$cmplx) + -qtl -> runs lapw2 and calculates QTL + -alm -> runs lapw2 and calculates ALM,BLM + -almd -> runs lapw2 and calculates ALM,BLM in lapw2 for DMFT (Aichhorn) +@@ -2546,11 +2547,11 @@ + -vresp-> runs lapw2 and creates case.vrespval (for TAU/meta-GGA) + -fermi-> runs lapw2 with FERMI switch + -efg -> runs lapw2 with EFG switch +--so -> runs lapw2/optic/spaghetti with def-file for spin-orbit calc. ++-so -> runs lapw2/optic/spaghetti with def-file for spin-orbit calc. + -hf -> runs lapw2 with Hartree-Fock/hybrid vectors + -diaghf -> calculates only the diagonal elements of HF Hamiltonian + -nonself -> calculates hf with Ex only (no eigenvalues/vectors) +--fbz -> runs kgen and generates a full mesh in the BZ ++-fbz -> runs kgen and generates a full mesh in the BZ + -fft -> runs dstart only up to case.in0_std creation + -super-> runs dstart and creates new_super.clmsum (and not $file.clmsum) + -lcore-> runs dstart with $file.rsplcore (produces $file.clmsc) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch new file mode 100644 index 0000000000..3800834f1b --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch @@ -0,0 +1,22 @@ +http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11158.html +--- WIEN2k_14.orig/SRC_lapw5/main1.f 2014-09-19 13:30:20.757390463 +0200 ++++ WIEN2k_14/SRC_lapw5/main1.f 2014-09-19 13:30:37.671774186 +0200 +@@ -346,7 +346,7 @@ + if(addsub.eq.' ADD') fadd=1.d0 + if(addsub.eq.' SUB') fadd=-1.d0 + +- IF(IUNIT.EQ.'ANG ') FAK=Bohr**3 ++ IF(IUNIT.EQ.'ANG ') FAK=1.D0/Bohr**3 ! Change to avoid altering lapw5 output (fix to WIEN2k 14.1): Was 6.7551d0 in WIEN2k 13.1 (and likely in verisons < 13.1) but changed to increase accuracy + R=VNORM(VX) + RELX=R + R=VNORM(VY) +@@ -373,7 +373,7 @@ + ! + ! Correct TCharge for units + if(UseSTM)then +- if(IUNIT.EQ.'ANG ')CTarget=CTarget/FAK ++ if(IUNIT.EQ.'ANG ')CTarget=CTarget*FAK ! Change to avoid altering output + ! Array for STM (LDM) + allocate(STM(NPX,NPY)) + endif + -- GitLab From 20e02bdd6d8648674c7c5d06cb44882d318d3a10 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 13:59:19 +0100 Subject: [PATCH 062/992] bcftools-1.1-goolf-1.4.10.eb --- .../b/bcftools/bcftools-1.1-goolf-1.4.10.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..7cdafdabd6 --- /dev/null +++ b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'bcftools' +version = '1.1' + +homepage = 'http://sourceforge.net/projects/samtools/' +description = """ utilities for variant calling and manipulating VCFs and BCFs """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/samtools/%(version)s', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +parallel = 1 + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bcftools", "plot-vcfstats", "vcfutils.pl"]], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 5a21cbf49efa11d287be4a3d9a9037936856e639 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 14:08:49 +0100 Subject: [PATCH 063/992] updated homepage --- easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb index 7cdafdabd6..f01baa3a62 100644 --- a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb @@ -6,7 +6,7 @@ name = 'bcftools' version = '1.1' -homepage = 'http://sourceforge.net/projects/samtools/' +homepage = 'http://www.htslib.org/' description = """ utilities for variant calling and manipulating VCFs and BCFs """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 0d6429b748258997e503a3d5bffcda38bd60ec88 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 14:12:10 +0100 Subject: [PATCH 064/992] updated description --- .../easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb index f01baa3a62..bbe68cc575 100644 --- a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb @@ -3,16 +3,17 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -name = 'bcftools' +name = 'BCFtools' version = '1.1' homepage = 'http://www.htslib.org/' -description = """ utilities for variant calling and manipulating VCFs and BCFs """ +description = """ Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising + SNP and short indel sequence variants """ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [('http://sourceforge.net/projects/samtools/files/samtools/%(version)s', 'download')] -sources = [SOURCE_TAR_BZ2] +sources = [SOURCELOWER_TAR_BZ2] dependencies = [('zlib', '1.2.8')] -- GitLab From 8df6608c234d23b05cc725a4284a6c646f224b42 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 14:12:34 +0100 Subject: [PATCH 065/992] renamed file --- ...{bcftools-1.1-goolf-1.4.10.eb => BCFtools-1.1-goolf-1.4.10.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/bcftools/{bcftools-1.1-goolf-1.4.10.eb => BCFtools-1.1-goolf-1.4.10.eb} (100%) diff --git a/easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bcftools/BCFtools-1.1-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/bcftools/bcftools-1.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/bcftools/BCFtools-1.1-goolf-1.4.10.eb -- GitLab From f6b67c22ae6a60e0c0a5114a1b192723c3fb97e2 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 14:15:38 +0100 Subject: [PATCH 066/992] renamed dir --- .../b/{bcftools => BCFtools}/BCFtools-1.1-goolf-1.4.10.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/{bcftools => BCFtools}/BCFtools-1.1-goolf-1.4.10.eb (100%) diff --git a/easybuild/easyconfigs/b/bcftools/BCFtools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/bcftools/BCFtools-1.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb -- GitLab From 887532fc2c252e8897c4e0ae52995fa190d0982b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 3 Nov 2014 09:37:22 +0100 Subject: [PATCH 067/992] 1 --- .../a/ATK/ATK-2.14.0-intel-2014b.eb | 30 +++++++++++++++ .../GDK-Pixbuf-2.30.7-intel-2014b.eb | 35 ++++++++++++++++++ ...Object-Introspection-1.42.0-intel-2014b.eb | 31 ++++++++++++++++ .../g/GTK+/GTK+-2.24.25-intel-2014b.eb | 33 +++++++++++++++++ .../p/Python/Python-2.7.8-intel-2014b.eb | 3 ++ ...Python-3.0.1.1-intel-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ 6 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb new file mode 100644 index 0000000000..24ac7dc408 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb @@ -0,0 +1,30 @@ +name = 'ATK' +version = '2.14.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ATK provides the set of accessibility interfaces that + are implemented by other toolkits and applications. Using + the ATK interfaces, accessibility tools have full access + to view and control running applications.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), +] + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.so'], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb new file mode 100644 index 0000000000..cbcafc7f3f --- /dev/null +++ b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb @@ -0,0 +1,35 @@ +name = 'GDK-Pixbuf' +version = '2.30.7' + +homepage = 'https://developer.gnome.org/gdx-pixbuf/' +description = """GdkPixbuf is a library for image loading and manipulation. + The GdkPixbuf documentation contains both + the programmer's guide and the API reference.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), + ('libjpeg-turbo', '1.3.1'), + ('libpng', '1.6.12'), + ('LibTIFF', '4.0.3'), +] + +configopts = '--with-x11 ' + +sanity_check_paths = { + 'files': ['bin/gdk-pixbuf-%s' % x for x in ['csource', 'pixdata', 'query-loaders']] + + ['lib/libgdk_pixbuf%s-2.0.so' % x for x in ['', '_xlib']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb new file mode 100644 index 0000000000..a7d8444e44 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb @@ -0,0 +1,31 @@ +name = 'GObject-Introspection' +version = '1.42.0' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), +] + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb new file mode 100644 index 0000000000..672e1ddf3e --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb @@ -0,0 +1,33 @@ +name = 'GTK+' +version = '2.24.25' + +homepage = 'http://www.gtk.org' +description = """GTK+, or the GIMP Toolkit, is a multi-platform toolkit + for creating graphical user interfaces. Offering a complete set of widgets, + GTK+ is suitable for projects ranging from small one-off tools + to complete application suites.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('Pango', '1.36.7'), + ('GObject-Introspection', '1.42.0'), + ('GDK-Pixbuf', '2.30.7'), + ('ATK', '2.14.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index fc03cf9418..76a6bcb647 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -90,6 +90,9 @@ exts_list = [ ('matplotlib', '1.3.1', { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], }), + ('pyamg', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyamg/'], + }), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..e75705dfa5 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +name = 'wxPython' +version = '3.0.1.1' + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] + +python = "Python" +pythonversion = '2.7.8' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libpng', '1.6.12'), + ('zlib', '1.2.8'), + ('libjpeg-turbo', '1.3.1'), + ('LibTIFF', '4.0.3'), + ('expat', '2.1.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 5ec7a8b7cf6b1356c442cb94c7289a8a935cbcbd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 5 Nov 2014 15:23:51 +0100 Subject: [PATCH 068/992] 2 --- .../b/Bison/Bison-2.5-intel-2014b.eb | 2 +- .../d/DBus/DBus-1.8.8-intel-2014b.eb | 22 ++++ .../dbus-glib/dbus-glib-0.102-intel-2014b.eb | 23 ++++ .../g/GConf/GConf-3.2.6-intel-2014b.eb | 34 ++++++ ...4b.eb => GDK-Pixbuf-2.30.8-intel-2014b.eb} | 2 +- .../GST-plugins-base-0.10.36-intel-2014b.eb | 32 ++++++ .../GStreamer-0.10.36-intel-2014b.eb | 36 ++++++ .../GStreamer/GStreamer-1.4.3-intel-2014b.eb | 38 ++++++ .../g/GTK+/GTK+-2.24.25-intel-2014b.eb | 7 +- .../i/intltool/intltool-0.50.2-intel-2014b.eb | 18 +++ .../l/libIDL/libIDL-0.8.14-intel-2014b.eb | 25 ++++ .../o/ORBit2/ORBit2-2.14.19-intel-2014b.eb | 25 ++++ .../o/ORBit2/ORBit2_2.14_fixgthread.patch | 24 ++++ ...Python-3.0.1.1-intel-2014b-Python-2.7.8.eb | 7 ++ .../w/wxPython/wxPython_3.0.1.1_intel.patch | 108 ++++++++++++++++++ 15 files changed, 398 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb rename easybuild/easyconfigs/g/GDK-Pixbuf/{GDK-Pixbuf-2.30.7-intel-2014b.eb => GDK-Pixbuf-2.30.8-intel-2014b.eb} (98%) create mode 100644 easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb create mode 100644 easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb create mode 100644 easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb create mode 100644 easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb index d87f069c2c..e4774cf7c1 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('M4', '1.4.16')] +builddependencies = [('M4', '1.4.17')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb new file mode 100644 index 0000000000..63bfd61c8d --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb @@ -0,0 +1,22 @@ +name = 'DBus' +version = '1.8.8' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', 'so']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb new file mode 100644 index 0000000000..a67144380a --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb @@ -0,0 +1,23 @@ +name = 'dbus-glib' +version = '0.102' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('DBus', '1.8.8'), + ('expat', '2.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.so', 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb new file mode 100644 index 0000000000..d3feb03c97 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb @@ -0,0 +1,34 @@ +name = 'GConf' +version = '3.2.6' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('dbus-glib', '0.102'), + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), + ('ORBit2', '2.14.19'), + ('intltool', '0.50.2'), +] + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb similarity index 98% rename from easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb rename to easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb index cbcafc7f3f..95ae4e8637 100644 --- a/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.7-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb @@ -1,5 +1,5 @@ name = 'GDK-Pixbuf' -version = '2.30.7' +version = '2.30.8' homepage = 'https://developer.gnome.org/gdx-pixbuf/' description = """GdkPixbuf is a library for image loading and manipulation. diff --git a/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb new file mode 100644 index 0000000000..cced46e20c --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb @@ -0,0 +1,32 @@ +name = 'GST-plugins-base' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +builddependencies = [ + ('Bison', '2.5'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-0.10' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-0.10.so' % x for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb new file mode 100644 index 0000000000..f10f413e57 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb @@ -0,0 +1,36 @@ +name = 'GStreamer' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('Bison', '2.5'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-0.10' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-0.10.so' % x for x in ['reamer', 'base', 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb new file mode 100644 index 0000000000..3cefe8bf97 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb @@ -0,0 +1,38 @@ +name = 'GStreamer' +version = '1.4.3' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.40.0'), + ('GObject-Introspection', '1.42.0'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), + ('M4', '1.4.17'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-1.0.so' % x for x in ['reamer', 'base', 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb index 672e1ddf3e..ab5dc7cedf 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb @@ -16,13 +16,14 @@ dependencies = [ ('GLib', '2.40.0'), ('Pango', '1.36.7'), ('GObject-Introspection', '1.42.0'), - ('GDK-Pixbuf', '2.30.7'), + ('GDK-Pixbuf', '2.30.8'), ('ATK', '2.14.0'), ] sanity_check_paths = { - 'files': [], - 'dirs': [] + 'files': ['bin/gtk-%s' % x for x in ['query-immodules-2.0', 'update-icon-cache', 'builder-convert', 'demo']] + + ['lib/libgailutil.so'] + ['lib/libg%sk-x11-2.0.so' % x for x in ['d','t']], + 'dirs': ['etc', 'include', 'share'] } modextrapaths = { diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb b/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb new file mode 100644 index 0000000000..a88c9eb891 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb @@ -0,0 +1,18 @@ +name = 'intltool' +version = '0.50.2' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of many + different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', 'ize', '-merge', '-prepare', '-update']], + 'dirs': ['share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb b/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb new file mode 100644 index 0000000000..be7a93b01a --- /dev/null +++ b/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb @@ -0,0 +1,25 @@ +name = 'libIDL' +version = '0.8.14' + +homepage = 'http://freecode.com/projects/libidl' +description = """libIDL is a library for creating trees of CORBA Interface Definition Language (IDL) + files, which is a specification for defining portable interfaces. libIDL was + initially written for ORBit (the ORB from the GNOME project, and the primaryi + means of libIDL distribution). However, the functionalityi + was designed to be as reusable and portable as possible.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/libIDL/%(version_major_minor)s'] +sources = [SOURCE_TAR_BZ2] + +dependencies = [ + ('GLib', '2.40.0'), +] + +sanity_check_paths = { + 'files': ['bin/libIDL-config-2', 'lib/libIDL-2.a', 'lib/libIDL-2.so'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb b/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb new file mode 100644 index 0000000000..bfbf9c366f --- /dev/null +++ b/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb @@ -0,0 +1,25 @@ +name = 'ORBit2' +version = '2.14.19' + +homepage = 'https://projects.gnome.org/ORBit2/' +description = """ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring mature C, C++ and Python bindings.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/ORBit2/%(version_major_minor)s'] +sources = [SOURCE_TAR_GZ] + +patches = ['ORBit2_%(version_major_minor)s_fixgthread.patch'] + +dependencies = [ + ('GLib', '2.40.0'), + ('libIDL', '0.8.14') +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ior-decode-2', 'linc-cleanup-sockets', 'orbit2-config', 'orbit-idl-2', 'typelib-dump']] + + ['lib/lib%s.%s' % (x,y) for x in ['ORBit-2', 'ORBitCosNaming-2', 'ORBit-imodule-2'] for y in ['a', 'so']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch b/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch new file mode 100644 index 0000000000..5d793515cd --- /dev/null +++ b/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch @@ -0,0 +1,24 @@ +# http://stackoverflow.com/questions/25590498/cannot-build-orbit2-fix-apparently-found-but-where-is-it +--- ORBit2-2.14.19.ORIG/linc2/src/Makefile.am 2010-02-09 13:05:35.000000000 +0100 ++++ ORBit2-2.14.19/linc2/src/Makefile.am 2014-11-03 16:58:20.518982441 +0100 +@@ -12,8 +12,7 @@ + -I$(top_builddir)/linc2/include \ + -I$(top_srcdir)/linc2/include \ + $(LINC_CFLAGS) \ +- $(WARN_CFLAGS) \ +- -DG_DISABLE_DEPRECATED ++ $(WARN_CFLAGS) + + if OS_WIN32 + else +--- ORBit2-2.14.19.ORIG/linc2/src/Makefile.in 2010-09-28 11:39:39.000000000 +0200 ++++ ORBit2-2.14.19/linc2/src/Makefile.in 2014-11-04 09:20:14.000518250 +0100 +@@ -244,7 +244,7 @@ + # -I$(top_srcdir)/include + INCLUDES = -I$(top_builddir)/linc2/include \ + -I$(top_srcdir)/linc2/include $(LINC_CFLAGS) $(WARN_CFLAGS) \ +- -DG_DISABLE_DEPRECATED $(am__append_1) ++ $(am__append_1) + liblinc_la_SOURCES = \ + linc.c \ + linc-connection.c \ diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb index e75705dfa5..00aefd6867 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-src-%(version)s.tar.bz2'] +patches = ['%(name)s_%(version)s_intel.patch'] + python = "Python" pythonversion = '2.7.8' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) @@ -27,8 +29,13 @@ dependencies = [ ('libjpeg-turbo', '1.3.1'), ('LibTIFF', '4.0.3'), ('expat', '2.1.0'), + ('GTK+', '2.24.25'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), ] +parallel = 1 + sanity_check_paths = { 'files': [], 'dirs': [] diff --git a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch new file mode 100644 index 0000000000..a69e52d13a --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch @@ -0,0 +1,108 @@ +# PATCH for intel compiler +# see http://trac.wxwidgets.org/ticket/15267 +# second part inspired by ---^ +# B. Hajgato Nov 04 2014 +--- wxPython-src-3.0.1.1.ORIG/Makefile.in 2014-06-24 23:43:01.000000000 +0200 ++++ wxPython-src-3.0.1.1/Makefile.in 2014-11-04 12:05:58.460396471 +0100 +@@ -16977,7 +16977,7 @@ + $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp + + monodll_extended.o: $(srcdir)/src/common/extended.c $(MONODLL_ODEP) +- $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/common/extended.c ++ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/common/extended.c + + monodll_ffile.o: $(srcdir)/src/common/ffile.cpp $(MONODLL_ODEP) + $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/common/ffile.cpp +@@ -22851,7 +22851,7 @@ + $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp + + monolib_extended.o: $(srcdir)/src/common/extended.c $(MONOLIB_ODEP) +- $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/common/extended.c ++ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/common/extended.c + + monolib_ffile.o: $(srcdir)/src/common/ffile.cpp $(MONOLIB_ODEP) + $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/common/ffile.cpp +@@ -28725,7 +28725,7 @@ + $(CXXC) -c -o $@ $(BASEDLL_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp + + basedll_extended.o: $(srcdir)/src/common/extended.c $(BASEDLL_ODEP) +- $(CCC) -c -o $@ $(BASEDLL_CFLAGS) $(srcdir)/src/common/extended.c ++ $(CXXC) -c -o $@ $(BASEDLL_CFLAGS) $(srcdir)/src/common/extended.c + + basedll_ffile.o: $(srcdir)/src/common/ffile.cpp $(BASEDLL_ODEP) + $(CXXC) -c -o $@ $(BASEDLL_CXXFLAGS) $(srcdir)/src/common/ffile.cpp +@@ -29241,7 +29241,7 @@ + $(CXXC) -c -o $@ $(BASELIB_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp + + baselib_extended.o: $(srcdir)/src/common/extended.c $(BASELIB_ODEP) +- $(CCC) -c -o $@ $(BASELIB_CFLAGS) $(srcdir)/src/common/extended.c ++ $(CXXC) -c -o $@ $(BASELIB_CFLAGS) $(srcdir)/src/common/extended.c + + baselib_ffile.o: $(srcdir)/src/common/ffile.cpp $(BASELIB_ODEP) + $(CXXC) -c -o $@ $(BASELIB_CXXFLAGS) $(srcdir)/src/common/ffile.cpp +#--- wxPython-src-3.0.1.1.ORIG/Makefile.in 2014-06-24 23:43:01.000000000 +0200 +#+++ wxPython-src-3.0.1.1/Makefile.in 2014-11-04 12:25:41.507128586 +0100 +#@@ -22653,13 +22653,13 @@ +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monodll_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(MONODLL_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monodll_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(MONODLL_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monodll_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(MONODLL_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monodll_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(MONODLL_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp +#@@ -28527,13 +28527,13 @@ +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monolib_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(MONOLIB_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monolib_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(MONOLIB_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monolib_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(MONOLIB_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monolib_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(MONOLIB_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp +#@@ -38955,13 +38955,13 @@ +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advdll_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(ADVDLL_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CCC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advdll_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(ADVDLL_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advdll_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(ADVDLL_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CCC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advdll_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(ADVDLL_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp +#@@ -39426,13 +39426,13 @@ +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advlib_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(ADVLIB_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CCC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advlib_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(ADVLIB_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advlib_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(ADVLIB_ODEP) +#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CCC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c +# +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advlib_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(ADVLIB_ODEP) +# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp -- GitLab From b26c3aaa4fa20e86f329b08ab27162a7dc34cacc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 5 Nov 2014 15:43:05 +0100 Subject: [PATCH 069/992] ncdf4 - netcdf4 for R 3.1.1 intel2014b --- .../n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb new file mode 100644 index 0000000000..cdf98f1940 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.13' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.1.1' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.3.2') +] + +moduleclass = 'math' -- GitLab From 98a44a2ff6ac5530414bd183076d2ab7d42a85a0 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Fri, 7 Nov 2014 16:57:34 +0000 Subject: [PATCH 070/992] Just bumping the bowtie version to the most recent. Compiles fine under goolf 1.4.10 Adding an author name so that users can complain more directly --- .../b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..0240ff0e2c --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +#Modified from existing version by: +#Robert Schmidt +#Ottawa Hospital Research Institute - Bioinformatics Team + +name = 'Bowtie' +version = '1.1.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' -- GitLab From fd60f5e07dc37691e637385e979077bbe211746c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 12 Nov 2014 10:58:52 +0100 Subject: [PATCH 071/992] 3 --- .../w/wxPython/wxPython_3.0.1.1_intel.patch | 120 ++---------------- 1 file changed, 12 insertions(+), 108 deletions(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch index a69e52d13a..f91d3210f4 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch +++ b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch @@ -1,108 +1,12 @@ -# PATCH for intel compiler -# see http://trac.wxwidgets.org/ticket/15267 -# second part inspired by ---^ -# B. Hajgato Nov 04 2014 ---- wxPython-src-3.0.1.1.ORIG/Makefile.in 2014-06-24 23:43:01.000000000 +0200 -+++ wxPython-src-3.0.1.1/Makefile.in 2014-11-04 12:05:58.460396471 +0100 -@@ -16977,7 +16977,7 @@ - $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp - - monodll_extended.o: $(srcdir)/src/common/extended.c $(MONODLL_ODEP) -- $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/common/extended.c -+ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/common/extended.c - - monodll_ffile.o: $(srcdir)/src/common/ffile.cpp $(MONODLL_ODEP) - $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/common/ffile.cpp -@@ -22851,7 +22851,7 @@ - $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp - - monolib_extended.o: $(srcdir)/src/common/extended.c $(MONOLIB_ODEP) -- $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/common/extended.c -+ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/common/extended.c - - monolib_ffile.o: $(srcdir)/src/common/ffile.cpp $(MONOLIB_ODEP) - $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/common/ffile.cpp -@@ -28725,7 +28725,7 @@ - $(CXXC) -c -o $@ $(BASEDLL_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp - - basedll_extended.o: $(srcdir)/src/common/extended.c $(BASEDLL_ODEP) -- $(CCC) -c -o $@ $(BASEDLL_CFLAGS) $(srcdir)/src/common/extended.c -+ $(CXXC) -c -o $@ $(BASEDLL_CFLAGS) $(srcdir)/src/common/extended.c - - basedll_ffile.o: $(srcdir)/src/common/ffile.cpp $(BASEDLL_ODEP) - $(CXXC) -c -o $@ $(BASEDLL_CXXFLAGS) $(srcdir)/src/common/ffile.cpp -@@ -29241,7 +29241,7 @@ - $(CXXC) -c -o $@ $(BASELIB_CXXFLAGS) $(srcdir)/src/common/evtloopcmn.cpp - - baselib_extended.o: $(srcdir)/src/common/extended.c $(BASELIB_ODEP) -- $(CCC) -c -o $@ $(BASELIB_CFLAGS) $(srcdir)/src/common/extended.c -+ $(CXXC) -c -o $@ $(BASELIB_CFLAGS) $(srcdir)/src/common/extended.c - - baselib_ffile.o: $(srcdir)/src/common/ffile.cpp $(BASELIB_ODEP) - $(CXXC) -c -o $@ $(BASELIB_CXXFLAGS) $(srcdir)/src/common/ffile.cpp -#--- wxPython-src-3.0.1.1.ORIG/Makefile.in 2014-06-24 23:43:01.000000000 +0200 -#+++ wxPython-src-3.0.1.1/Makefile.in 2014-11-04 12:25:41.507128586 +0100 -#@@ -22653,13 +22653,13 @@ -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monodll_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(MONODLL_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monodll_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(MONODLL_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monodll_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(MONODLL_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CCC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monodll_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(MONODLL_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONODLL_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp -#@@ -28527,13 +28527,13 @@ -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monolib_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(MONOLIB_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@monolib_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(MONOLIB_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2_USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monolib_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(MONOLIB_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CCC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@monolib_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(MONOLIB_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION__USE_GUI_1@ $(CXXC) -c -o $@ $(MONOLIB_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp -#@@ -38955,13 +38955,13 @@ -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advdll_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(ADVDLL_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CCC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advdll_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(ADVDLL_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advdll_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(ADVDLL_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CCC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVDLL_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advdll_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(ADVDLL_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVDLL_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp -#@@ -39426,13 +39426,13 @@ -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_3@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk/taskbar.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advlib_gtk_eggtrayicon.o: $(srcdir)/src/gtk/eggtrayicon.c $(ADVLIB_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CCC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@advlib_hildon_notifmsg.o: $(srcdir)/src/gtk/hildon/notifmsg.cpp $(ADVLIB_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_2@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk/hildon/notifmsg.cpp -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advlib_gtk1_eggtrayicon.o: $(srcdir)/src/gtk1/eggtrayicon.c $(ADVLIB_ODEP) -#-@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CCC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -#+@COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVLIB_CFLAGS) $(srcdir)/src/gtk1/eggtrayicon.c -# -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@advlib_gtk1_taskbar.o: $(srcdir)/src/gtk1/taskbar.cpp $(ADVLIB_ODEP) -# @COND_TOOLKIT_GTK_TOOLKIT_VERSION_@ $(CXXC) -c -o $@ $(ADVLIB_CXXFLAGS) $(srcdir)/src/gtk1/taskbar.cpp +# Intel compiler have problems with precompiled headers (cannot mix C and C++ precompiled headers, like in GNU compilers) +# B. Hajgato Nov 07 2014 +--- wxPython-src-3.0.1.1.ORIG/build/tools/build-wxwidgets.py 2014-01-04 22:08:37.000000000 +0100 ++++ wxPython-src-3.0.1.1/build/tools/build-wxwidgets.py 2014-11-07 14:02:02.144031589 +0100 +@@ -265,6 +265,7 @@ + configure_opts.append("--with-osx_cocoa") + + wxpy_configure_opts = [ ++ "--disable-precomp-headers", + "--with-opengl", + "--enable-sound", + "--enable-graphics_ctx", -- GitLab From 6ce40a54a62e04bdd6dd4a10f9c4fdfef3672440 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 13 Nov 2014 11:05:49 +0100 Subject: [PATCH 072/992] Update to NWChem 6.5 --- ...243-intel-2014b-2014-09-10-Python-2.7.8.eb | 31 +++++++++++++++++++ ...Chem-6.5.revision26243-parallelbuild.patch | 29 +++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb new file mode 100644 index 0000000000..2eefc9a7f3 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb @@ -0,0 +1,31 @@ +name = 'NWChem' +version = '6.5.revision26243' + +homepage = 'http://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'i8': True} + +source_urls = [ 'http://www.nwchem-sw.org/download.php?f='] +verdate = '2014-09-10' +sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] + +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-%(version)s-parallelbuild.patch', +] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s-%s' % (verdate, python, pyver) +dependencies = [(python, pyver)] + +modules = 'all python' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch new file mode 100644 index 0000000000..8558fe4778 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch @@ -0,0 +1,29 @@ +--- src/config/makefile.h.orig 2014-09-10 20:08:39.000000000 +0200 ++++ src/config/makefile.h 2014-11-12 11:33:06.449137413 +0100 +@@ -1394,7 +1394,7 @@ + CORE_SUBDIRS_EXTRA = blas lapack + CC = gcc + RANLIB = ranlib +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + INSTALL = @echo $@ is built + CPP = gcc -E -nostdinc -undef -P + FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1814,7 +1814,7 @@ + endif + endif + DEFINES += -DEXT_INT +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + _CPU = $(shell uname -m ) + ifeq ($(BLAS_LIB),) + CORE_SUBDIRS_EXTRA += blas +@@ -1923,7 +1923,7 @@ + endif # end of ia32 bit + ifeq ($(_CPU),x86_64) + # +- MAKEFLAGS = -j 2 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + COPTIMIZE = -O1 + ifeq ($(NWCHEM_TARGET),CATAMOUNT) + FC=pgf90 -- GitLab From a8d699b11c25fa0f9eef01317e97c076653ef451 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 13 Nov 2014 16:43:53 +0100 Subject: [PATCH 073/992] No vec-report, please --- ...Chem-6.5.revision26243-parallelbuild.patch | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch index 8558fe4778..c3a7a32982 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch @@ -1,5 +1,16 @@ +# corrected parallel builds, no debug info and no vec reports +# B. Hajgato Nov 13 2014 --- src/config/makefile.h.orig 2014-09-10 20:08:39.000000000 +0200 +++ src/config/makefile.h 2014-11-12 11:33:06.449137413 +0100 +@@ -1231,7 +1231,7 @@ + _FC=ifort + #ifort 9.1 + # LINK.f = ifort $(LDFLAGS) +- FOPTIONS += -align -mp1 -w -g -vec-report1 ++ FOPTIONS += -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif @@ -1394,7 +1394,7 @@ CORE_SUBDIRS_EXTRA = blas lapack CC = gcc @@ -9,6 +20,24 @@ INSTALL = @echo $@ is built CPP = gcc -E -nostdinc -undef -P FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1527,7 +1527,7 @@ + DEFINES += -DGFORTRAN + endif + ifeq ($(_FC),ifc) +- FOPTIONS = -align -mp1 -w -g -vec-report1 ++ FOPTIONS = -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1602,7 +1602,7 @@ + endif + + ifeq ($(CC),icc) +- COPTIONS = -mp1 -w -g -vec-report1 ++ COPTIONS = -mp1 -w + COPTIMIZE = -O3 -unroll + ifeq ($(_CPU),i586) + COPTIMIZE += -tpp5 -xi # this are for PentiumII @@ -1814,7 +1814,7 @@ endif endif @@ -27,3 +56,37 @@ COPTIMIZE = -O1 ifeq ($(NWCHEM_TARGET),CATAMOUNT) FC=pgf90 +@@ -1959,19 +1959,17 @@ + ifeq ($(_IFCV15ORNEWER), Y) + FOPTIONS += -qopt-report-file=stderr + ifdef USE_OPTREPORT +- FOPTIONS += -qopt-report=1 -qopt-report-phase=vec ++ FOPTIONS += -qopt-report=0 -qopt-report-phase=vec + endif + ifdef USE_OPENMP + FOPTIONS += -qopenmp +- FOPTIONS += -qopt-report-phase=openmp + COPTIONS += -qopenmp + DEFINES+= -DUSE_OPENMP + endif + else +- FOPTIONS += -vec-report6 ++ FOPTIONS += -vec-report0 + ifdef USE_OPENMP + FOPTIONS += -openmp +- FOPTIONS += -openmp-report2 + COPTIONS += -openmp + DEFINES+= -DUSE_OPENMP + endif +@@ -2086,9 +2084,9 @@ + ICCV15ORNEWER=$(shell icc -V 2>&1|egrep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 15) {print "Y";exit}}') + COPTIONS += -xHOST -ftz + ifeq ($(ICCV15ORNEWER), Y) +- COPTIONS += -qopt-report-phase:openmp -vec-report=1 ++ COPTIONS += -qopt-report-phase:openmp + else +- COPTIONS += -openmp-report=2 -vec-report=1 ++ COPTIONS += -openmp-report0 + endif + #old COPTIMIZE = -O3 -hlo -mP2OPT_hlo_level=2 + COPTIMIZE = -O3 -- GitLab From 9aafec03d3092d979d73f1d276e14adb2319db2a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 19 Nov 2014 16:05:29 +0100 Subject: [PATCH 074/992] HTSeq for intel-2014b plus version bump --- .../HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..1f11e79748 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.6.1p1' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) +eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%s/site-packages/%s" % (pyshortver, eggname)], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'data' -- GitLab From c0bb88458cd4a7001b66d7cddb4459b98f5bff8e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 28 Nov 2014 14:30:34 +0100 Subject: [PATCH 075/992] 3 --- ...rcuitscape-4.0-intel-2014b-Python-2.7.8.eb | 35 +++++++++++++++++++ ...thonCard-0.8.2-intel-2014b-Python-2.7.8.eb | 31 ++++++++++++++++ ...Python-3.0.1.1-intel-2014b-Python-2.7.8.eb | 10 ++++-- 3 files changed, 74 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..1285fae586 --- /dev/null +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'Circuitscape' +version = '4.0.5' + +homepage = 'http://www.circuitscape.org/' +description = """Circuitscape is a free, open-source program which borrows algorithms + from electronic circuit theory to predict patterns of movement, gene flow, + and genetic differentiation among plant and animal populations in + heterogeneous landscapes. Circuit theory complements least-cost path + approaches because it considers effects of all possible pathways + across a landscape simultaneously.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('PythonCard', '0.8.2', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(namelower)s/__init__.py' % pyshortver] + + ['bin/cs%s.py' % x for x in ['run', 'verify']], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..4343c60c4e --- /dev/null +++ b/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'PythonCard' +version = '0.8.2' + +homepage = 'http://pythoncard.sourceforge.net/' +description = """PythonCard is a GUI construction kit for building cross-platform desktop + applications on Windows, Mac OS X, and Linux, using the Python language.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('wxPython', '3.0.1.1', versionsuffix), +] +exts_filter = ('python -c "import PythonCard"', "") + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%s/__init__.py' % (pyshortver,name)], + 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver,name)], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb index 00aefd6867..c4c88fa0d8 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb @@ -37,8 +37,14 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': [], - 'dirs': [] + 'files': ['bin/wxrc'] + + ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + + ['lib/lib%s-3.0.so' % x for x in ['wx_baseu', 'wx_gtk2u_core']], + 'dirs': ['include', 'share', 'lib/python%s/site-packages' % pythonshortversion ] +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%s/site-packages/wx-3.0-gtk2' % pythonshortversion ], } moduleclass = 'vis' -- GitLab From e1554e9905795b3df9e05173cf111b5a4e429978 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:33:57 +0100 Subject: [PATCH 076/992] Added Boost for ictce-7.1.2 --- .../Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb new file mode 100644 index 0000000000..d29dcc1cda --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['intellinuxjam_fPIC.patch', 'boost-impi5.patch'] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' -- GitLab From 72bbdc9bd8a170dabd0a835f31d962bb84a890bb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:34:59 +0100 Subject: [PATCH 077/992] Added GROMACS 5.0.2 --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb new file mode 100644 index 0000000000..5e23be1026 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.2' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '2.8.12'), + ('libxml2', '2.9.1') +] + +dependencies = [('Boost', '1.55.0', '-Python-2.7.8')] + +moduleclass = 'bio' -- GitLab From ffae6d949021809817926cfc0514897cea9bfcb5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 13:50:39 +0100 Subject: [PATCH 078/992] Added forgotten Boost patch --- .../easyconfigs/b/Boost/boost-impi5.patch | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/boost-impi5.patch diff --git a/easybuild/easyconfigs/b/Boost/boost-impi5.patch b/easybuild/easyconfigs/b/Boost/boost-impi5.patch new file mode 100644 index 0000000000..635da12964 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/boost-impi5.patch @@ -0,0 +1,37 @@ +diff -ur boost_1_55_0.orig/tools/build/v2/tools/mpi.jam boost_1_55_0/tools/build/v2/tools/mpi.jam +--- boost_1_55_0.orig/tools/build/v2/tools/mpi.jam 2012-04-26 23:32:41.000000000 +0200 ++++ boost_1_55_0/tools/build/v2/tools/mpi.jam 2014-09-03 13:45:45.000000000 +0200 +@@ -301,6 +301,16 @@ + } + # OpenMPI and newer versions of LAM-MPI have -showme:compile and + # -showme:link. ++ # Look for MPICH ++ else if [ safe-shell-command "$(command) -show" ] ++ { ++ if $(.debug-configuration) ++ { ++ ECHO "Found MPICH wrapper compiler: $(command)" ; ++ } ++ compile_flags = [ SHELL "$(command) -compile_info" ] ; ++ link_flags = [ SHELL "$(command) -link_info" ] ; ++ } + else if [ safe-shell-command "$(command) -showme:compile" ] && + [ safe-shell-command "$(command) -showme:link" ] + { +@@ -327,16 +337,6 @@ + + result = [ SHELL "$(command) -showme" ] ; + } +- # Look for MPICH +- else if [ safe-shell-command "$(command) -show" ] +- { +- if $(.debug-configuration) +- { +- ECHO "Found MPICH wrapper compiler: $(command)" ; +- } +- compile_flags = [ SHELL "$(command) -compile_info" ] ; +- link_flags = [ SHELL "$(command) -link_info" ] ; +- } + # Sun HPC and Ibm POE + else if [ SHELL "$(command) -v 2>/dev/null" ] + { -- GitLab From 6f7529dc84bb7a7dc452d75b5bbba05eb5dfd330 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Dec 2014 09:20:44 +0100 Subject: [PATCH 079/992] Circuitscape4 --- .../a/ATK/ATK-2.14.0-intel-2014b.eb | 30 ----------- .../b/Bison/Bison-2.5-intel-2014b.eb | 2 +- ...itscape-4.0.5-intel-2014b-Python-2.7.8.eb} | 1 - .../d/DBus/DBus-1.8.8-intel-2014b.eb | 22 -------- .../dbus-glib/dbus-glib-0.102-intel-2014b.eb | 23 --------- .../g/GConf/GConf-3.2.6-intel-2014b.eb | 34 ------------- .../GDK-Pixbuf-2.30.8-intel-2014b.eb | 35 ------------- ...Object-Introspection-1.42.0-intel-2014b.eb | 31 ------------ .../GST-plugins-base-0.10.36-intel-2014b.eb | 32 ------------ .../GStreamer-0.10.36-intel-2014b.eb | 36 ------------- .../GStreamer/GStreamer-1.4.3-intel-2014b.eb | 38 -------------- .../g/GTK+/GTK+-2.24.25-intel-2014b.eb | 34 ------------- .../i/intltool/intltool-0.50.2-intel-2014b.eb | 18 ------- .../l/libIDL/libIDL-0.8.14-intel-2014b.eb | 25 ---------- .../o/ORBit2/ORBit2-2.14.19-intel-2014b.eb | 25 ---------- .../o/ORBit2/ORBit2_2.14_fixgthread.patch | 24 --------- ...thonCard-0.8.2-intel-2014b-Python-2.7.8.eb | 31 ------------ ...Python-3.0.1.1-intel-2014b-Python-2.7.8.eb | 50 ------------------- .../w/wxPython/wxPython_3.0.1.1_intel.patch | 12 ----- 19 files changed, 1 insertion(+), 502 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb rename easybuild/easyconfigs/c/Circuitscape/{Circuitscape-4.0-intel-2014b-Python-2.7.8.eb => Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb} (96%) delete mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch delete mode 100644 easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb delete mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb delete mode 100644 easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb deleted file mode 100644 index 24ac7dc408..0000000000 --- a/easybuild/easyconfigs/a/ATK/ATK-2.14.0-intel-2014b.eb +++ /dev/null @@ -1,30 +0,0 @@ -name = 'ATK' -version = '2.14.0' - -homepage = 'https://developer.gnome.org/atk/' -description = """ATK provides the set of accessibility interfaces that - are implemented by other toolkits and applications. Using - the ATK interfaces, accessibility tools have full access - to view and control running applications.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), -] - -sanity_check_paths = { - 'files': ['lib/libatk-1.0.so'], - 'dirs': ['include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb index e4774cf7c1..d87f069c2c 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('M4', '1.4.17')] +builddependencies = [('M4', '1.4.16')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb similarity index 96% rename from easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb rename to easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb index 1285fae586..a07b1584dc 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb @@ -23,7 +23,6 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), - ('PythonCard', '0.8.2', versionsuffix), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb deleted file mode 100644 index 63bfd61c8d..0000000000 --- a/easybuild/easyconfigs/d/DBus/DBus-1.8.8-intel-2014b.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'DBus' -version = '1.8.8' - -homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' -description = """D-Bus is a message bus system, a simple way for applications to talk - to one another. In addition to interprocess communication, D-Bus helps - coordinate process lifecycle; it makes it simple and reliable to code - a "single instance" application or daemon, and to launch applications - and daemons on demand when their services are needed.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://dbus.freedesktop.org/releases/dbus'] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + - ['lib/libdbus-1.%s' % x for x in ['a', 'so']], - 'dirs': ['include', 'share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb deleted file mode 100644 index a67144380a..0000000000 --- a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.102-intel-2014b.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'dbus-glib' -version = '0.102' - -homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' -description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('DBus', '1.8.8'), - ('expat', '2.1.0'), -] - -sanity_check_paths = { - 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.so', 'lib/libdbus-glib-1.a'], - 'dirs': ['include', 'share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb deleted file mode 100644 index d3feb03c97..0000000000 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2014b.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'GConf' -version = '3.2.6' - -homepage = 'https://projects.gnome.org/gconf/' -description = """GConf is a system for storing application preferences. - It is intended for user preferences; not configuration - of something like Apache, or arbitrary data storage.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] -sources = [SOURCE_TAR_XZ] - -dependencies = [ - ('dbus-glib', '0.102'), - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), - ('ORBit2', '2.14.19'), - ('intltool', '0.50.2'), -] - -sanity_check_paths = { - 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + - ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + - ['lib/libgconf-2.%s' % x for x in['a', 'so']], - 'dirs': ['include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb b/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb deleted file mode 100644 index 95ae4e8637..0000000000 --- a/easybuild/easyconfigs/g/GDK-Pixbuf/GDK-Pixbuf-2.30.8-intel-2014b.eb +++ /dev/null @@ -1,35 +0,0 @@ -name = 'GDK-Pixbuf' -version = '2.30.8' - -homepage = 'https://developer.gnome.org/gdx-pixbuf/' -description = """GdkPixbuf is a library for image loading and manipulation. - The GdkPixbuf documentation contains both - the programmer's guide and the API reference.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), - ('libjpeg-turbo', '1.3.1'), - ('libpng', '1.6.12'), - ('LibTIFF', '4.0.3'), -] - -configopts = '--with-x11 ' - -sanity_check_paths = { - 'files': ['bin/gdk-pixbuf-%s' % x for x in ['csource', 'pixdata', 'query-loaders']] + - ['lib/libgdk_pixbuf%s-2.0.so' % x for x in ['', '_xlib']], - 'dirs': ['include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb deleted file mode 100644 index a7d8444e44..0000000000 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.42.0-intel-2014b.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'GObject-Introspection' -version = '1.42.0' - -homepage = 'https://wiki.gnome.org/GObjectIntrospection/' -description = """GObject introspection is a middleware layer between C libraries - (using GObject) and language bindings. The C library can be scanned at - compile time and generate a metadata file, in addition to the actual - native C library. Then at runtime, language bindings can read this - metadata and automatically provide bindings to call into the C library.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), -] - -sanity_check_paths = { - 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + - ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], - 'dirs': ['include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb deleted file mode 100644 index cced46e20c..0000000000 --- a/easybuild/easyconfigs/g/GStreamer/GST-plugins-base-0.10.36-intel-2014b.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'GST-plugins-base' -version = '0.10.36' - -homepage = 'http://gstreamer.freedesktop.org/' -description = """GStreamer is a library for constructing graphs of media-handling - components. The applications it supports range from simple - Ogg/Vorbis playback, audio/video streaming to complex audio - (mixing) and video (non-linear editing) processing.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [('GStreamer', '0.10.36')] - -builddependencies = [ - ('Bison', '2.5'), -] - -sanity_check_paths = { - 'files': ['bin/gst-%s-0.10' % x for x in ['discoverer', 'visualise']] + - ['lib/libgst%s-0.10.so' % x for x in ['app', 'audio', 'video']], - 'dirs': ['include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb deleted file mode 100644 index f10f413e57..0000000000 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2014b.eb +++ /dev/null @@ -1,36 +0,0 @@ -name = 'GStreamer' -version = '0.10.36' - -homepage = 'http://gstreamer.freedesktop.org/' -description = """GStreamer is a library for constructing graphs of media-handling - components. The applications it supports range from simple - Ogg/Vorbis playback, audio/video streaming to complex audio - (mixing) and video (non-linear editing) processing.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), - ('zlib', '1.2.8'), -] - -builddependencies = [ - ('Bison', '2.5'), -] - -sanity_check_paths = { - 'files': ['bin/gst-%s-0.10' % x for x in ['inspect', 'typefind', 'launch']] + - ['lib/libgst%s-0.10.so' % x for x in ['reamer', 'base', 'controller', 'check']], - 'dirs': ['include', 'share', 'libexec'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb deleted file mode 100644 index 3cefe8bf97..0000000000 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.4.3-intel-2014b.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'GStreamer' -version = '1.4.3' - -homepage = 'http://gstreamer.freedesktop.org/' -description = """GStreamer is a library for constructing graphs of media-handling - components. The applications it supports range from simple - Ogg/Vorbis playback, audio/video streaming to complex audio - (mixing) and video (non-linear editing) processing.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('GObject-Introspection', '1.42.0'), - ('zlib', '1.2.8'), -] - -builddependencies = [ - ('Bison', '3.0.2'), - ('flex', '2.5.39'), - ('M4', '1.4.17'), -] - -sanity_check_paths = { - 'files': ['bin/gst-%s-1.0' % x for x in ['inspect', 'typefind', 'launch']] + - ['lib/libgst%s-1.0.so' % x for x in ['reamer', 'base', 'controller', 'check']], - 'dirs': ['include', 'share', 'libexec'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb deleted file mode 100644 index ab5dc7cedf..0000000000 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.25-intel-2014b.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'GTK+' -version = '2.24.25' - -homepage = 'http://www.gtk.org' -description = """GTK+, or the GIMP Toolkit, is a multi-platform toolkit - for creating graphical user interfaces. Offering a complete set of widgets, - GTK+ is suitable for projects ranging from small one-off tools - to complete application suites.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(namelower)s/%(version_major_minor)s/'] -sources = [SOURCELOWER_TAR_XZ] - -dependencies = [ - ('GLib', '2.40.0'), - ('Pango', '1.36.7'), - ('GObject-Introspection', '1.42.0'), - ('GDK-Pixbuf', '2.30.8'), - ('ATK', '2.14.0'), -] - -sanity_check_paths = { - 'files': ['bin/gtk-%s' % x for x in ['query-immodules-2.0', 'update-icon-cache', 'builder-convert', 'demo']] + - ['lib/libgailutil.so'] + ['lib/libg%sk-x11-2.0.so' % x for x in ['d','t']], - 'dirs': ['etc', 'include', 'share'] -} - -modextrapaths = { - 'GI_TYPELIB_PATH': 'share', - 'XDG_DATA_DIRS': 'share', -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb b/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb deleted file mode 100644 index a88c9eb891..0000000000 --- a/easybuild/easyconfigs/i/intltool/intltool-0.50.2-intel-2014b.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'intltool' -version = '0.50.2' - -homepage = 'http://freedesktop.org/wiki/Software/intltool/' -description = """intltool is a set of tools to centralize translation of many - different file formats using GNU gettext-compatible PO files.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download'] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['bin/intltool%s' % x for x in ['-extract', 'ize', '-merge', '-prepare', '-update']], - 'dirs': ['share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb b/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb deleted file mode 100644 index be7a93b01a..0000000000 --- a/easybuild/easyconfigs/l/libIDL/libIDL-0.8.14-intel-2014b.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'libIDL' -version = '0.8.14' - -homepage = 'http://freecode.com/projects/libidl' -description = """libIDL is a library for creating trees of CORBA Interface Definition Language (IDL) - files, which is a specification for defining portable interfaces. libIDL was - initially written for ORBit (the ORB from the GNOME project, and the primaryi - means of libIDL distribution). However, the functionalityi - was designed to be as reusable and portable as possible.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/libIDL/%(version_major_minor)s'] -sources = [SOURCE_TAR_BZ2] - -dependencies = [ - ('GLib', '2.40.0'), -] - -sanity_check_paths = { - 'files': ['bin/libIDL-config-2', 'lib/libIDL-2.a', 'lib/libIDL-2.so'], - 'dirs': ['include', 'share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb b/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb deleted file mode 100644 index bfbf9c366f..0000000000 --- a/easybuild/easyconfigs/o/ORBit2/ORBit2-2.14.19-intel-2014b.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'ORBit2' -version = '2.14.19' - -homepage = 'https://projects.gnome.org/ORBit2/' -description = """ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring mature C, C++ and Python bindings.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/ORBit2/%(version_major_minor)s'] -sources = [SOURCE_TAR_GZ] - -patches = ['ORBit2_%(version_major_minor)s_fixgthread.patch'] - -dependencies = [ - ('GLib', '2.40.0'), - ('libIDL', '0.8.14') -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['ior-decode-2', 'linc-cleanup-sockets', 'orbit2-config', 'orbit-idl-2', 'typelib-dump']] + - ['lib/lib%s.%s' % (x,y) for x in ['ORBit-2', 'ORBitCosNaming-2', 'ORBit-imodule-2'] for y in ['a', 'so']], - 'dirs': ['include', 'share'] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch b/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch deleted file mode 100644 index 5d793515cd..0000000000 --- a/easybuild/easyconfigs/o/ORBit2/ORBit2_2.14_fixgthread.patch +++ /dev/null @@ -1,24 +0,0 @@ -# http://stackoverflow.com/questions/25590498/cannot-build-orbit2-fix-apparently-found-but-where-is-it ---- ORBit2-2.14.19.ORIG/linc2/src/Makefile.am 2010-02-09 13:05:35.000000000 +0100 -+++ ORBit2-2.14.19/linc2/src/Makefile.am 2014-11-03 16:58:20.518982441 +0100 -@@ -12,8 +12,7 @@ - -I$(top_builddir)/linc2/include \ - -I$(top_srcdir)/linc2/include \ - $(LINC_CFLAGS) \ -- $(WARN_CFLAGS) \ -- -DG_DISABLE_DEPRECATED -+ $(WARN_CFLAGS) - - if OS_WIN32 - else ---- ORBit2-2.14.19.ORIG/linc2/src/Makefile.in 2010-09-28 11:39:39.000000000 +0200 -+++ ORBit2-2.14.19/linc2/src/Makefile.in 2014-11-04 09:20:14.000518250 +0100 -@@ -244,7 +244,7 @@ - # -I$(top_srcdir)/include - INCLUDES = -I$(top_builddir)/linc2/include \ - -I$(top_srcdir)/linc2/include $(LINC_CFLAGS) $(WARN_CFLAGS) \ -- -DG_DISABLE_DEPRECATED $(am__append_1) -+ $(am__append_1) - liblinc_la_SOURCES = \ - linc.c \ - linc-connection.c \ diff --git a/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb deleted file mode 100644 index 4343c60c4e..0000000000 --- a/easybuild/easyconfigs/p/PythonCard/PythonCard-0.8.2-intel-2014b-Python-2.7.8.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = "PythonPackage" - -name = 'PythonCard' -version = '0.8.2' - -homepage = 'http://pythoncard.sourceforge.net/' -description = """PythonCard is a GUI construction kit for building cross-platform desktop - applications on Windows, Mac OS X, and Linux, using the Python language.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -python = 'Python' -pythonver = '2.7.8' -pyshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) - -dependencies = [ - (python, pythonver), - ('wxPython', '3.0.1.1', versionsuffix), -] -exts_filter = ('python -c "import PythonCard"', "") - -sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%s/__init__.py' % (pyshortver,name)], - 'dirs': ['lib/python%s/site-packages/%s' % (pyshortver,name)], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb deleted file mode 100644 index c4c88fa0d8..0000000000 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.1.1-intel-2014b-Python-2.7.8.eb +++ /dev/null @@ -1,50 +0,0 @@ -name = 'wxPython' -version = '3.0.1.1' - -homepage = 'http://www.wxpython.org' -description = """wxPython is a GUI toolkit for the Python programming language. - It allows Python programmers to create programs with a robust, - highly functional graphical user interface, simply and easily. - It is implemented as a Python extension module (native code) - that wraps the popular wxWidgets cross platform GUI library, - which is written in C++.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s-src-%(version)s.tar.bz2'] - -patches = ['%(name)s_%(version)s_intel.patch'] - -python = "Python" -pythonversion = '2.7.8' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - -dependencies = [ - (python, pythonversion), - ('libpng', '1.6.12'), - ('zlib', '1.2.8'), - ('libjpeg-turbo', '1.3.1'), - ('LibTIFF', '4.0.3'), - ('expat', '2.1.0'), - ('GTK+', '2.24.25'), - ('GConf', '3.2.6'), - ('GST-plugins-base', '0.10.36'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/wxrc'] + - ['bin/py%s' % x for x in ['alacarte', 'alamode', 'crust', 'shell', 'wrap', 'wxrc']] + - ['lib/lib%s-3.0.so' % x for x in ['wx_baseu', 'wx_gtk2u_core']], - 'dirs': ['include', 'share', 'lib/python%s/site-packages' % pythonshortversion ] -} - -modextrapaths = { - 'PYTHONPATH': ['lib/python%s/site-packages/wx-3.0-gtk2' % pythonshortversion ], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch b/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch deleted file mode 100644 index f91d3210f4..0000000000 --- a/easybuild/easyconfigs/w/wxPython/wxPython_3.0.1.1_intel.patch +++ /dev/null @@ -1,12 +0,0 @@ -# Intel compiler have problems with precompiled headers (cannot mix C and C++ precompiled headers, like in GNU compilers) -# B. Hajgato Nov 07 2014 ---- wxPython-src-3.0.1.1.ORIG/build/tools/build-wxwidgets.py 2014-01-04 22:08:37.000000000 +0100 -+++ wxPython-src-3.0.1.1/build/tools/build-wxwidgets.py 2014-11-07 14:02:02.144031589 +0100 -@@ -265,6 +265,7 @@ - configure_opts.append("--with-osx_cocoa") - - wxpy_configure_opts = [ -+ "--disable-precomp-headers", - "--with-opengl", - "--enable-sound", - "--enable-graphics_ctx", -- GitLab From b85d1c25f711fd686a68e0b949c4ddc96a3ab93e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:03:42 +0100 Subject: [PATCH 080/992] Update DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb --- .../d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index ca812f75ef..facf14e7e4 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -15,7 +15,10 @@ perl = 'Perl' perlver = '5.20.0' versionsuffix = '-%s-%s' % (perl, perlver) -dependencies = [(perl, perlver), ("PostgreSQL", "9.3.5")] +dependencies = [ + (perl, perlver), + ("PostgreSQL", "9.3.5") +] options = {'modulename': 'DBD::Pg'} -- GitLab From 4d7b48d4445c3f6bdfe814b192939a7ea471c927 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:05:28 +0100 Subject: [PATCH 081/992] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 9b40199a4f..33c2f00038 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -16,7 +16,10 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [ + ('openssl-devel', + 'libssl-dev') +] java = 'Java' javaver = '1.7.0_60' @@ -25,6 +28,7 @@ dependencies = [ (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), +# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ -- GitLab From cbf893e6a96a5c2c5e5031fe46e3e1f857ff221f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:05:47 +0100 Subject: [PATCH 082/992] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 33c2f00038..0adb8caf54 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -28,7 +28,7 @@ dependencies = [ (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), -# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ -- GitLab From 60481d2dbba84675f5352ce5129dfc6319e19d7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:09:08 +0100 Subject: [PATCH 083/992] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 0adb8caf54..b5c98f2a72 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -16,10 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [ - ('openssl-devel', - 'libssl-dev') -] +osdependencies = [('openssl-devel', 'libssl-dev')] java = 'Java' javaver = '1.7.0_60' -- GitLab From f1e903f9e87acbcc338bff1f99dc0c79a15a66b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Tue, 16 Dec 2014 09:20:04 +0100 Subject: [PATCH 084/992] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index b5c98f2a72..f0f5501b84 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'PostgreSQL' version = '9.3.5' -- GitLab From fbe18fa83394133ca1a1601ec15a01396a4a7280 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 13:03:04 +0100 Subject: [PATCH 085/992] All deps for gnuplot 5 with intel-2015a --- .../c/cairo/cairo-1.12.18-intel-2015a.eb | 29 +++++++++++++++++ .../e/expat/expat-2.1.0-intel-2015a.eb | 15 +++++++++ .../fontconfig-2.11.1-intel-2015a.eb | 22 +++++++++++++ .../f/freetype/freetype-2.5.5-intel-2015a.eb | 21 +++++++++++++ .../libjpeg-turbo-1.4.0-intel-2015a.eb | 24 ++++++++++++++ .../l/libpng/libpng-1.6.16-intel-2015a.eb | 19 ++++++++++++ .../n/NASM/NASM-2.11.06-intel-2015a.eb | 31 +++++++++++++++++++ .../p/pixman/pixman-0.32.6-intel-2015a.eb | 20 ++++++++++++ 8 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb new file mode 100644 index 0000000000..e43e75307f --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.12.18' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. +Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, +PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('libpng', '1.6.16'), + ('freetype', '2.5.5'), + ('zlib', '1.2.8'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('expat', '2.1.0'), + ('bzip2', '1.0.6'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb new file mode 100644 index 0000000000..0eb1188648 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb new file mode 100644 index 0000000000..a8f2612b6a --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb new file mode 100644 index 0000000000..3f93bd6070 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.16')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb new file mode 100644 index 0000000000..639a4e904b --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb new file mode 100644 index 0000000000..23292508e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb new file mode 100644 index 0000000000..88003caecd --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb new file mode 100644 index 0000000000..480001289a --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.32.6' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 2bdc74f8dacb175fddf22ea06495f54ece3236fc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 13:03:28 +0100 Subject: [PATCH 086/992] Gnuplot 5 for intel-2014b and intel-2015a --- .../g/gnuplot/gnuplot-5.0.0-intel-2014b.eb | 35 +++++++++++++++++++ .../g/gnuplot/gnuplot-5.0.0-intel-2015a.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb new file mode 100644 index 0000000000..e30d4a22d3 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb new file mode 100644 index 0000000000..8f7d80279e --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 441dd17e18b9dffa536fe73cd3aa5ee70db3642e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 14:18:56 +0100 Subject: [PATCH 087/992] Added autoconf for intel 2015a --- .../a/Autoconf/Autoconf-2.69-intel-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb new file mode 100644 index 0000000000..a3c280daab --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically + configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like + systems without manual user intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From d24528dc73eec74272050e5dcf06876c35a902a5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 14:19:13 +0100 Subject: [PATCH 088/992] Updated cairo to work around pthread detection issues --- .../c/cairo/cairo-1.12.18-intel-2015a.eb | 6 ++++++ .../c/cairo/cairo-1.12.18-pthread-check.patch | 17 +++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index e43e75307f..d051b99544 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,6 +23,12 @@ dependencies = [ ('bzip2', '1.0.6'), ] +builddependencies = [('autoconf', '2.69')] + +patches = ['cairo-1.12.18-pthread-check.patch'] + +preconfigopts = " autoconf configure.ac > configure && " + # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC configopts = "--enable-symbol-lookup=no" diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch new file mode 100644 index 0000000000..20821e7211 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch @@ -0,0 +1,17 @@ +# Make sure the configure script doesn't fail over a 'no version information available' warning +# by wpoely86@gmail.com +diff -ur cairo-1.12.18.orig/build/aclocal.cairo.m4 cairo-1.12.18/build/aclocal.cairo.m4 +--- cairo-1.12.18.orig/build/aclocal.cairo.m4 2013-03-15 21:29:27.000000000 +0100 ++++ cairo-1.12.18/build/aclocal.cairo.m4 2015-01-14 14:08:01.000000000 +0100 +@@ -101,9 +101,9 @@ + $1 + AC_LINK_IFELSE( + [AC_LANG_SOURCE([$_compile_program])], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` + cairo_cc_flag=yes], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` + cairo_cc_flag=no]) + + if test "x$cairo_cc_stderr" != "x"; then -- GitLab From 9701985a5c4b5e603263bed5d39ff6bfa557dc5c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 14:20:55 +0100 Subject: [PATCH 089/992] Fix typo in cairo --- easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index d051b99544..c3b27fffcb 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [('autoconf', '2.69')] +builddependencies = [('Autoconf', '2.69')] patches = ['cairo-1.12.18-pthread-check.patch'] -- GitLab From 22feb6bfe7fafec7f5e1dbf667ea9aff4ef0e70e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 16:52:23 +0100 Subject: [PATCH 090/992] Stupid stupid stupid error in patch --- .../easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch index 20821e7211..9019afb946 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch @@ -8,10 +8,10 @@ diff -ur cairo-1.12.18.orig/build/aclocal.cairo.m4 cairo-1.12.18/build/aclocal.c AC_LINK_IFELSE( [AC_LANG_SOURCE([$_compile_program])], - [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` -+ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` cairo_cc_flag=yes], - [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` -+ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` cairo_cc_flag=no]) if test "x$cairo_cc_stderr" != "x"; then -- GitLab From 8024913b322f6757649f0c2e12594a3a3188973b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 23 Jan 2015 17:13:38 +0100 Subject: [PATCH 091/992] Enable UTF-8 in ncurses --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 3bcfd50e3f..52d037a115 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -12,4 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# enable UTF-8 version of ncurses +configopts = '--enable-widec ' + moduleclass = 'devel' -- GitLab From 6aae2b595d2f9e7d909a5f6cf08ff98f6e3492f6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 23 Jan 2015 17:52:00 +0100 Subject: [PATCH 092/992] Build libncurses and libncursesw --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 52d037a115..0cd975654f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# enable UTF-8 version of ncurses -configopts = '--enable-widec ' +# build the normal library and the UTF-8 version +configopts = ['', '--enable-widec '] moduleclass = 'devel' -- GitLab From 04539511825fd537874a74a8d2bc8157891c4f0e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 24 Jan 2015 13:53:57 +0100 Subject: [PATCH 093/992] Another try for ncursesw --- .../easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 0cd975654f..b52538d409 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -12,7 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# build the normal library and the UTF-8 version -configopts = ['', '--enable-widec '] +configopts = [ +# the regular version + '--enable-pc-files', +# the UTF-8 enabled version (ncursesw) + '--enable-pc-files --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] moduleclass = 'devel' -- GitLab From 8752a28c823ec55f6a21f615e49a45877230642a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 24 Jan 2015 14:10:27 +0100 Subject: [PATCH 094/992] drop pkg-config in ncurses --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index b52538d409..3ec3f49a07 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -14,9 +14,9 @@ sources = [SOURCE_TAR_GZ] configopts = [ # the regular version - '--enable-pc-files', + '', # the UTF-8 enabled version (ncursesw) - '--enable-pc-files --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' -- GitLab From 35266d8655bfa26924a951417b616c6f08716a21 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 26 Jan 2015 20:24:01 +0100 Subject: [PATCH 095/992] Fix remarks --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 3ec3f49a07..867d190ac8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -13,9 +13,9 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] configopts = [ -# the regular version + # default build, no custom configure options '', -# the UTF-8 enabled version (ncursesw) + # the UTF-8 enabled version (ncursesw) '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] -- GitLab From 5d2d1b0b9cc82f64abf00ff3b5d87caaaf46ef86 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 26 Jan 2015 20:31:40 +0100 Subject: [PATCH 096/992] Enable for ncursesw in all ncurses easyconfigs --- .../n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 7 +++++++ .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 7 +++++++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 7 +++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 7 +++++++ 40 files changed, 280 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 3522f8a87b..612e7244e4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index f954a9b12a..0bc9dc079e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 6a10d2ec63..30ff4e9d12 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 4913ef008f..d637ceb09f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -14,6 +14,13 @@ sources = [SOURCE_TGZ] # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 8b7d3a2416..ecedc6d59c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 1632ef23de..44555aa4d2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 43375f2a29..6b107ae408 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index ad58285a85..eeca718a41 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index f972b6a4ff..7ed33f8631 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 5f56a55621..b72a2c5545 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index cd59ae4ab3..ee2b0ee573 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 52e0aac9ea..e7e371cbeb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 78b7618284..fc7e428415 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index b4ea71f97f..caaf4d94b5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index 2f9501c9ae..cd83ef60ce 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index 15745294d9..fc5b9a327c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 062cbaeab6..ef9c9fdf56 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -14,6 +14,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index a372492a64..1e42213c88 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -12,6 +12,13 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 38b356d5e1..1a4bf4b720 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 947e8e3afa..33d8114b0a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 4084c938c1..38625bc5af 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 33bb21037f..9cd547f787 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index e67f480463..f6221718e5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 5a698183f4..794f3cf9ff 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 4e33e95089..51c7c4637d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index c0284ad94f..0da2bc399e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 95388cfc5b..51e89fabbe 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 731485e77b..efe819bc41 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 8cb79c351b..b1d6ed583b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index ee127c7a3c..7acb72a025 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 020778b318..411d761488 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index a81155369d..e647ee8ca9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index 84c486d4d9..b4ba551660 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index ab5e8538f3..2a4e97a56d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -14,4 +14,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 2a7094da21..5585b5f946 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 4aface2738..3084b14d4f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 867d190ac8..51bee3bd1f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -19,4 +19,11 @@ configopts = [ '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 9963e053c2..3442fd88ba 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index decfe9bc04..e40599e242 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index f4b42632c9..75c66a9c2a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -12,4 +12,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + moduleclass = 'devel' -- GitLab From d2cd0fe9eb7b32c8354c03f184e05fed63348885 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 09:45:08 +0100 Subject: [PATCH 097/992] We are gonna drop the block for ncurses --- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 2 ++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 2 ++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 2 ++ 40 files changed, 80 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 612e7244e4..c1bbc1841f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 0bc9dc079e..4e4d33f99e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 30ff4e9d12..175c730746 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index d637ceb09f..5d25cf6a2c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index ecedc6d59c..74e5f9d664 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 44555aa4d2..54ecc2aa20 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 6b107ae408..923b64a2b1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index eeca718a41..d656ee0065 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 7ed33f8631..2a34cb02bd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index b72a2c5545..7172901875 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index ee2b0ee573..8dcd07e56e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index e7e371cbeb..fe078dec07 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index fc7e428415..f56f2e2f3f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index caaf4d94b5..fbcfb30bca 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index cd83ef60ce..8a0a0a6686 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index fc5b9a327c..ef641196aa 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index ef9c9fdf56..bead5d5548 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index 1e42213c88..a80072cffd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 1a4bf4b720..16c3de6193 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 33d8114b0a..fe409e6bef 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 38625bc5af..109ffe0762 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 9cd547f787..013e826233 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index f6221718e5..d98d2224a8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 794f3cf9ff..04d9e09dc8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 51c7c4637d..cbbffabdf6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 0da2bc399e..d2814a64a5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 51e89fabbe..312ebedf9f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index efe819bc41..2fe6cb142e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index b1d6ed583b..e3bb6acc60 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 7acb72a025..22f9c52166 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 411d761488..738094a8e2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index e647ee8ca9..cda26334d3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index b4ba551660..b2f405273f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index 2a4e97a56d..c42c316754 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 5585b5f946..d205c60702 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 3084b14d4f..7893f29d3f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 867d190ac8..94883afa9c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 3442fd88ba..b9054c4126 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index e40599e242..980ddeeb1b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 75c66a9c2a..a0cd6ba12f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' -- GitLab From c192f7c59f8286b812de97bdbf7ed49fff7fafcf Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 09:49:50 +0100 Subject: [PATCH 098/992] Add darwin patch everywhere for ncurses --- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 5 ++++- .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 3 +++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 3 +++ .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 3 +++ .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 3 +++ .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 3 +++ .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 3 +++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 3 +++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 3 +++ 40 files changed, 121 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index c1bbc1841f..d6014c322a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 4e4d33f99e..340e451aec 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 175c730746..04ba4525a8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 5d25cf6a2c..1ebda09767 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -11,10 +11,13 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} toolchainopts = {'optarch': True, 'pic': True} -sources = [SOURCE_TGZ] # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] +sources = [SOURCE_TGZ] + +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ # default build, no custom configure options diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 74e5f9d664..d0b0145611 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 54ecc2aa20..463bfe470b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 923b64a2b1..f717055d33 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index d656ee0065..10513a3220 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 2a34cb02bd..c713d9a1f0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 7172901875..de5fe067af 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 7a01c335e9..1120c00075 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -17,6 +17,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index fe078dec07..6fe83c6278 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index f56f2e2f3f..3b2a8be253 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index fbcfb30bca..016a0e7ba7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index 8a0a0a6686..ad1db40db0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index ef641196aa..b7eac5dc3b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index bead5d5548..32697687bd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index a80072cffd..8f42fa1df4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 16c3de6193..6adba21388 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index fe409e6bef..71be12db82 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 109ffe0762..b2bd02a79f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 013e826233..f43ac7b793 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index d98d2224a8..d485cb49cb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 04d9e09dc8..fac41c78c8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index cbbffabdf6..3b5e2ad161 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index d2814a64a5..9591d9dd15 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 312ebedf9f..807f4ac478 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 2fe6cb142e..0b83eb7d69 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index e3bb6acc60..35aab70c78 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 22f9c52166..440b759444 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 738094a8e2..de9ab95d93 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index cda26334d3..dd539c41ee 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index b2f405273f..96658e9de5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index c42c316754..fbd2501cb3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -16,6 +16,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index d205c60702..77555deb61 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 7893f29d3f..5e21a72951 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 94883afa9c..4d5679832e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index b9054c4126..edb162762e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index 980ddeeb1b..f9e31b4951 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index a0cd6ba12f..531773e338 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -14,6 +14,9 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +patches = ['ncurses-5.9_configure_darwin.patch'] + configopts = [ # default build, no custom configure options '', -- GitLab From a70b0dbf432dc6396924c5fdbf5a92e236c6961f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 09:54:00 +0100 Subject: [PATCH 099/992] Use same configopts as in easyblock --- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 6 +++--- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 6 +++--- .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 6 +++--- .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 6 +++--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 6 +++--- .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 6 +++--- 40 files changed, 120 insertions(+), 120 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index d6014c322a..bb5656e2a6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 340e451aec..c886fe843f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 04ba4525a8..ebbfaa4116 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 1ebda09767..5c607404c1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index d0b0145611..1a855ba2bc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 463bfe470b..5323795d31 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index f717055d33..98be0d4c70 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TGZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index 10513a3220..d4b7a59d96 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index c713d9a1f0..998a5e97ab 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index de5fe067af..53f116fa2e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 1120c00075..a086acf239 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -21,10 +21,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 6fe83c6278..7e4ecbfbb4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 3b2a8be253..55ed8d26f6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 016a0e7ba7..5ee673d106 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index ad1db40db0..e805cd9d17 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index b7eac5dc3b..d6f07984c3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 32697687bd..80481a982f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index 8f42fa1df4..ef647ff36e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 6adba21388..b25da04d34 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 71be12db82..465f64143f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index b2bd02a79f..e60406ef3b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index f43ac7b793..2342cdf598 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index d485cb49cb..8131a3deb8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index fac41c78c8..4320090d62 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 3b5e2ad161..058e2d911f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 9591d9dd15..3fc4dbeb15 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 807f4ac478..bcd27e8b03 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 0b83eb7d69..e757256ace 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 35aab70c78..40ba8d73af 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 440b759444..1483b7bf55 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index de9ab95d93..fb0453b4df 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index dd539c41ee..583d73732b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index 96658e9de5..1eb6d03b2a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index fbd2501cb3..ada5615af2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -20,10 +20,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 77555deb61..b24af21a1d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 5e21a72951..282c1bb362 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 4d5679832e..9423467931 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index edb162762e..40ddbfa412 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index f9e31b4951..868c6a2548 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 531773e338..76893f1192 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -18,10 +18,10 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] moduleclass = 'devel' -- GitLab From 765d0211bafdbff648e3571c80867a89e292dd82 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 09:57:57 +0100 Subject: [PATCH 100/992] Move patch comment into patch --- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 1 - .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 1 - .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 2 -- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 1 - .../easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch | 2 ++ 41 files changed, 2 insertions(+), 41 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index bb5656e2a6..54e14d2a5b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index c886fe843f..c1f0ff7fd5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index ebbfaa4116..875f56a51e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 5c607404c1..ce47ae5e0b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 1a855ba2bc..98c94f5e9e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 5323795d31..1bf10071f6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 98be0d4c70..2b21c09a91 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index d4b7a59d96..192d513a80 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 998a5e97ab..974b0ae6ed 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 53f116fa2e..2d67efa2d5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index a086acf239..1d7c5cc5a2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -8,7 +8,6 @@ description = """The Ncurses (new curses) library is a free software emulation o and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] toolchain = {'name': 'GCC', 'version': '4.8.2'} @@ -17,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 7e4ecbfbb4..4b3eee0442 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 55ed8d26f6..8181599cdf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 5ee673d106..4db2c80086 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index e805cd9d17..d17f763573 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index d6f07984c3..f3056c6cc3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 80481a982f..6482090fe7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index ef647ff36e..729623bbc5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index b25da04d34..783353a5e6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 465f64143f..1f7cb3f66e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index e60406ef3b..432e92f67a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 2342cdf598..23ac474bfd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index 8131a3deb8..7b855b2439 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 4320090d62..0aaaa39fd8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 058e2d911f..988166fe3c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 3fc4dbeb15..101d3a39be 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index bcd27e8b03..509cfc629d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index e757256ace..e4a369e4a4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 40ba8d73af..9a1bd44ae0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 1483b7bf55..dbc54a911d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index fb0453b4df..97ad47cdc7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index 583d73732b..350c62963e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index 1eb6d03b2a..ad40bd7b81 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index ada5615af2..3421c52995 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -16,7 +16,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index b24af21a1d..27921a13b6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 282c1bb362..3059b1ba1a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 9423467931..ff0d85d604 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 40ddbfa412..1e51ebbe9c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index 868c6a2548..bc591b2935 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 76893f1192..d48f6b822e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -14,7 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html patches = ['ncurses-5.9_configure_darwin.patch'] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch index cbc78d120b..19a1f77d5b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch @@ -1,3 +1,5 @@ +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +# by Fotis --- ncurses-5.9.orig/configure 2014-10-25 21:11:31.000000000 +0200 +++ ncurses-5.9/configure 2014-10-25 21:11:10.000000000 +0200 @@ -5584,7 +5584,7 @@ -- GitLab From f6d433f619a6eeba900ef89d1683db553b258794 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 10:03:14 +0100 Subject: [PATCH 101/992] New sanity check for ncurses --- .../easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index ff0d85d604..4912fd41da 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' -- GitLab From 070cce48b60e412dff94e34b1b9ac74dfc9429ef Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Jan 2015 10:18:38 +0100 Subject: [PATCH 102/992] Added sanity check everywhere --- .../n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 10 ++++++++++ .../ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 10 ++++++++++ .../n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 10 ++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 10 ++++++++++ 39 files changed, 390 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 54e14d2a5b..6d40fe65a5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index c1f0ff7fd5..7d2df71a8f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 875f56a51e..a971bf0cc9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index ce47ae5e0b..360335ba07 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 98c94f5e9e..021bbd904f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 1bf10071f6..439c4ca406 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 2b21c09a91..1fcb38e69b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index 192d513a80..399dc72d43 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index 974b0ae6ed..bcf8a1dcfa 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 2d67efa2d5..d967731cf4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 1d7c5cc5a2..9608f82f81 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -25,4 +25,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 4b3eee0442..6bf4c2b332 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 8181599cdf..6313c884fc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 4db2c80086..727175a0e9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index d17f763573..26e6ab54bf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index f3056c6cc3..c993267096 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 6482090fe7..38361f94f7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -28,4 +28,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index 729623bbc5..b057182b0c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -26,4 +26,14 @@ configopts = [ # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 783353a5e6..d67bdf2770 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 1f7cb3f66e..169534ccd8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 432e92f67a..7e1f5ce19f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 23ac474bfd..2df180dac8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index 7b855b2439..c31fdc08ca 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 0aaaa39fd8..bfba6b87fe 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 988166fe3c..76b20bd13a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 101d3a39be..1cb1b2fa6b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 509cfc629d..cf54b65a18 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index e4a369e4a4..7ee6110e8d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 9a1bd44ae0..5753a19c6f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index dbc54a911d..7466ea8529 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 97ad47cdc7..2df3b61306 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index 350c62963e..0d8611a193 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index ad40bd7b81..ce62d53ca0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index 3421c52995..017c395992 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -25,4 +25,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 27921a13b6..b6a67863ad 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 3059b1ba1a..edb943229c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 1e51ebbe9c..389a334b0b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index bc591b2935..ab5729d6df 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index d48f6b822e..1a23dd3813 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -23,4 +23,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' -- GitLab From f4c8416d21a83206b93adef5d30cc93331af8243 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 18:38:11 +0000 Subject: [PATCH 103/992] Building an older version of Cufflinks for users that like the older format --- .../Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 42 +++++++++++++++++ .../c/Cufflinks/cufflinks-1.3.0-ldflags.patch | 45 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..2eca2eb6ac --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Cufflinks' +version = "1.3.0" # tweaked by EasyBuild (was: '2.0.2') + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.18'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +patches = ['Cufflinks_GCC-4.7.patch', 'cufflinks-1.3.0-ldflags.patch'] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch new file mode 100644 index 0000000000..9c2bd9e9a2 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch @@ -0,0 +1,45 @@ +diff -ru cufflinks-1.3.0/configure cufflinks-1.3.0_patched/configure +--- cufflinks-1.3.0/configure 2012-01-02 13:36:44.000000000 +0000 ++++ cufflinks-1.3.0_patched/configure 2015-01-27 18:32:24.810282390 +0000 +@@ -6386,7 +6386,8 @@ + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" + CXXFLAGS="$CFLAGS" + CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS" +-LDFLAGS="$ext_LDFLAGS" ++user_LDFLAGS="$LDFLAGS" ++LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" + + # Checks for structures/functions that can be used to determine system memory + echo "$as_me:$LINENO: checking for struct sysinfo.totalram" >&5 +diff -ru cufflinks-1.3.0/src/Makefile.in cufflinks-1.3.0_patched/src/Makefile.in +--- cufflinks-1.3.0/src/Makefile.in 2012-01-02 13:36:43.000000000 +0000 ++++ cufflinks-1.3.0_patched/src/Makefile.in 2015-01-27 18:20:02.944386541 +0000 +@@ -438,24 +438,24 @@ + # (echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@ + cufflinks_SOURCES = cufflinks.cpp + cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cufflinks_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) ++cufflinks_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) + cuffcompare_SOURCES = cuffcompare.cpp + cuffcompare_LDADD = libgc.a + gffread_SOURCES = gffread.cpp + gffread_LDADD = libgc.a + cuffdiff_SOURCES = cuffdiff.cpp + cuffdiff_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cuffdiff_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++cuffdiff_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + gtf_to_sam_SOURCES = gtf_to_sam.cpp + gtf_to_sam_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-gtf_to_sam_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++gtf_to_sam_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + #cuffcluster_SOURCES = cuffcluster.cpp + #cuffcluster_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) + #cuffcluster_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + compress_gtf_SOURCES = compress_gtf.cpp + compress_gtf_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-compress_gtf_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++compress_gtf_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + all: all-am + + .SUFFIXES: -- GitLab From 6f4ac9178ba8ad044f765c67cdc1b215b03cb18f Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 18:46:15 +0000 Subject: [PATCH 104/992] removing a bad comment --- .../easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 2eca2eb6ac..60d2ee4a72 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -11,7 +11,7 @@ ## name = 'Cufflinks' -version = "1.3.0" # tweaked by EasyBuild (was: '2.0.2') +version = "1.3.0" homepage = 'http://cufflinks.cbcb.umd.edu/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" -- GitLab From 55c4a267adec324bb0ba120fcc5c08921e0481a6 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 20:18:33 +0000 Subject: [PATCH 105/992] some style changes --- .../c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 7 +++++-- ...nks-1.3.0-ldflags.patch => cufflinks-1.x-ldflags.patch} | 0 2 files changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/Cufflinks/{cufflinks-1.3.0-ldflags.patch => cufflinks-1.x-ldflags.patch} (100%) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 60d2ee4a72..d03c8b241d 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -16,8 +16,8 @@ version = "1.3.0" homepage = 'http://cufflinks.cbcb.umd.edu/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" -toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} +toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] @@ -29,7 +29,10 @@ dependencies = [ ('zlib', '1.2.7'), ] -patches = ['Cufflinks_GCC-4.7.patch', 'cufflinks-1.3.0-ldflags.patch'] +patches = [ + 'Cufflinks_GCC-4.7.patch', + 'cufflinks-1.x-ldflags.patch' +] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' diff --git a/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch similarity index 100% rename from easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch rename to easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch -- GitLab From 6bf1b6cd4d227abefce167ec9eaf533d5ad0098c Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 20:21:24 +0000 Subject: [PATCH 106/992] whoops, inverted wrong line --- .../easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index d03c8b241d..96199f4bf2 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -16,8 +16,8 @@ version = "1.3.0" homepage = 'http://cufflinks.cbcb.umd.edu/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" -toolchainopts = {'optarch': True, 'pic': True} toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] @@ -34,8 +34,8 @@ patches = [ 'cufflinks-1.x-ldflags.patch' ] -configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { 'files': ['bin/cufflinks'], -- GitLab From 19e1b5d2c5e2d4b897291483f9469a641a06e170 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 28 Jan 2015 09:10:38 +0100 Subject: [PATCH 107/992] Added intel easyconfig for SAMtools --- .../s/SAMtools/SAMtools-1.1-intel-2015a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb new file mode 100644 index 0000000000..91e58c27f0 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'SAMtools' +version = '1.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' -- GitLab From 088c20eb5e6a8756cf380d5ead691f3be15e8f3e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:32:22 +0100 Subject: [PATCH 108/992] fosss-2015.01: with zlib & binutils --- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 39 ++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2015.01.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb new file mode 100644 index 0000000000..7266051e56 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -0,0 +1,39 @@ +easyblock = "Toolchain" + +name = 'foss' +version = '2015.01' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_version = '4.9.2' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build goolf dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, + ('zlib', '1.2.8', '', comp), + ('binutils', '2.25', '', comp), + ('OpenMPI', '1.8.4', '', comp), + (blaslib, blasver, blassuff, comp), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' -- GitLab From 9991a4e9bd90acedd99b0146f84c94d87cdcbd5c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:38:12 +0100 Subject: [PATCH 109/992] New gompi with zlib & binutils --- easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb | 24 +++++++++++++++++++ .../easyconfigs/g/gompi/gompi-2015.01.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2015.01.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb new file mode 100644 index 0000000000..f50cd40115 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb @@ -0,0 +1,24 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '1.9.0' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.2' +comp = (compname, compver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('zlib', '1.2.8', '', comp), + ('binutils', '2.25', '', comp), + ('OpenMPI', '1.8.4', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb new file mode 100644 index 0000000000..e59112cb7f --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb @@ -0,0 +1,24 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2015.01' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.2' +comp = (compname, compver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('zlib', '1.2.8', '', comp), + ('binutils', '2.25', '', comp), + ('OpenMPI', '1.8.4', '', comp), +] + +moduleclass = 'toolchain' -- GitLab From cd2a6f815f46bf2983e3a11795f5def1d3e7033c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:38:33 +0100 Subject: [PATCH 110/992] New goolf & foss with zlib & binutils --- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 2 +- easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb | 39 ++++++++++++++++++++ 2 files changed, 40 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb index 7266051e56..411ab43736 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -18,7 +18,7 @@ blasver = '0.2.13' blas = '%s-%s' % (blaslib, blasver) blassuff = '-LAPACK-3.5.0' -# toolchain used to build goolf dependencies +# toolchain used to build foss dependencies comp_mpi_tc_name = 'gompi' comp_mpi_tc_ver = "%s" % version comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb new file mode 100644 index 0000000000..0f2aea75a4 --- /dev/null +++ b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb @@ -0,0 +1,39 @@ +easyblock = "Toolchain" + +name = 'goolf' +version = '1.9.0' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_version = '4.9.2' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build goolf dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, + ('zlib', '1.2.8', '', comp), + ('binutils', '2.25', '', comp), + ('OpenMPI', '1.8.4', '', comp), + (blaslib, blasver, blassuff, comp), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' -- GitLab From 6c8f97284b062e5dcb9ab7b6e1a327bef6114255 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:39:59 +0100 Subject: [PATCH 111/992] New FFTW easyconfigs for new gompi's --- .../f/FFTW/FFTW-3.3.4-gompi-2015.01.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb new file mode 100644 index 0000000000..080b817838 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '1.9.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 2132b1deeb371d18baa424cac1d498990d31bad9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:44:22 +0100 Subject: [PATCH 112/992] New scalapack easyconfigs --- ...ompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 25 +++++++++++++++++++ ...pi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..e0aff023b0 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '1.9.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.2'))] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..962d8049d0 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2015.01'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.2'))] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 8c06ce5366b6903de62cbd3af0af18cf0bc0a1e9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:44:54 +0100 Subject: [PATCH 113/992] New FFTW easyconfigs --- .../f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb | 34 +++++++++++++++++++ .../f/FFTW/FFTW-3.3.4-gompi-2015.01.eb | 2 +- 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb new file mode 100644 index 0000000000..080b817838 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '1.9.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb index 080b817838..bcb190c092 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb @@ -7,7 +7,7 @@ homepage = 'http://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'gompi', 'version': '1.9.0'} +toolchain = {'name': 'gompi', 'version': '2015.01'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -- GitLab From 0c4f936088ed782fc5a6793fd03b87deb6cc6ee6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 15:11:27 +0100 Subject: [PATCH 114/992] Added HPL for new foss & goolf --- .../easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb | 18 ++++++++++++++++++ .../easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb new file mode 100644 index 0000000000..6e2eb261d6 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2015.01'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb new file mode 100644 index 0000000000..e9fc6dc2e2 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'goolf', 'version': '1.9.0'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 45bf598d8b7ac24c166c738bad6a8a8a3094be6c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 17:26:33 +0100 Subject: [PATCH 115/992] Added some additional comment in the MacOSX patch --- .../easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch index 19a1f77d5b..293f47532a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch @@ -1,5 +1,5 @@ # in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html -# by Fotis +# tried/proposed by Fotis, meant for MacOSX compatible ncurses builds... --- ncurses-5.9.orig/configure 2014-10-25 21:11:31.000000000 +0200 +++ ncurses-5.9/configure 2014-10-25 21:11:10.000000000 +0200 @@ -5584,7 +5584,7 @@ -- GitLab From 076d8971e8f5043c0b611168a9c389b51373a6aa Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 29 Jan 2015 14:13:25 +0100 Subject: [PATCH 116/992] Drop preconfigopts from zlib We don't know why it's there and it seems to be messing up the `zlib.map` inclusion. --- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb index 1b3b05c520..73e6b29017 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From 997f1baf47f0ce8120d6d442d130ca08269b752d Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 29 Jan 2015 14:34:46 +0000 Subject: [PATCH 117/992] a foss-2015a version of Cufflinks-2.2.1 --- .../Boost-1.55.0-foss-2015a-Python-2.7.9.eb | 25 ++++++++++++++++ .../c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb | 29 +++++++++++++++++++ .../e/Eigen/Eigen-3.2.3-foss-2015a.eb | 14 +++++++++ .../s/SAMtools/SAMtools-0.1.19-foss-2015a.eb | 21 ++++++++++++++ 4 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..88a81a73e9 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb new file mode 100644 index 0000000000..7ae5cdce38 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -0,0 +1,29 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cole-trapnell-lab.github.io/cufflinks/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + # issues with boost > 1.55, see https://github.com/cole-trapnell-lab/cufflinks/issues/3 + ('Boost', '1.55.0', '-Python-2.7.9'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.2.3'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb new file mode 100644 index 0000000000..a2767dc205 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.3' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb new file mode 100644 index 0000000000..c7a055062e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'SAMtools' +version = '0.1.19' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' -- GitLab From 9d7b3d81fb4b342881becb00d0f9f779523b0864 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 29 Jan 2015 14:38:28 +0000 Subject: [PATCH 118/992] switching order of config and preconfig --- easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb index 7ae5cdce38..d0372e6f70 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -18,8 +18,8 @@ dependencies = [ ('zlib', '1.2.8'), ] -configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { 'files': ['bin/cufflinks'], -- GitLab From cb72e773d51856979c831d9db1028820e8c5bf46 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 08:49:58 +0100 Subject: [PATCH 119/992] Added intel easyconfig for FFTW --- .../f/FFTW/FFTW-3.3.4-intel-2015a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb new file mode 100644 index 0000000000..ce8a9b16ca --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +# see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 637e3228cd649088160ee6a0fd40567507c5ba8c Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 09:15:00 +0100 Subject: [PATCH 120/992] Added foss easyconfig for PCRE --- .../p/PCRE/PCRE-8.36-foss-2015a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb new file mode 100644 index 0000000000..d43a790e2f --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.36' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +configopts = "--with-pic --disable-cpp" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'devel' -- GitLab From c4874fee095c749e5e7d5a20ba3d8da01c85c0cc Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 13:22:39 +0100 Subject: [PATCH 121/992] Added foss easyconfig for Octave --- .../o/Octave/Octave-3.8.2-foss-2015a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb new file mode 100644 index 0000000000..150b37eaf0 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -0,0 +1,26 @@ +name = 'Octave' +version = '3.8.2' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftpmirror.gnu.org/octave/'] + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +configopts = ['--with-blas="-lopenblas"'] + +dependencies = [ + ('PCRE', '8.36'), + ('ncurses', '5.9'), + ('libreadline', '6.3'), +] + +moduleclass = 'math' + -- GitLab From 54343d8faebbeaeb61054461be98e36e4bbe25d9 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 13:55:26 +0100 Subject: [PATCH 122/992] Fixed style issues as per request --- .../easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index 150b37eaf0..25b2a7b0a9 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -9,11 +9,6 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/octave/'] -sanity_check_paths = { - 'files': ['bin/octave'], - 'dirs': [] -} - configopts = ['--with-blas="-lopenblas"'] dependencies = [ @@ -22,5 +17,9 @@ dependencies = [ ('libreadline', '6.3'), ] -moduleclass = 'math' +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} +moduleclass = 'math' -- GitLab From 277d7e0dbf695d7c9b417e342661f9e95ebf4a6d Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 13:55:56 +0100 Subject: [PATCH 123/992] Fixed style issues as per request --- easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb index d43a790e2f..dd7d330b7c 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb @@ -12,9 +12,9 @@ description = """ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' -- GitLab From f448096adc29c302039c50a5c4b556614e3ef04f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Feb 2015 14:10:41 +0100 Subject: [PATCH 124/992] Add usefull comment about binutils --- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb index 411ab43736..dfce67f25b 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -26,6 +26,7 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # compiler toolchain depencies # we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain # because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ comp, ('zlib', '1.2.8', '', comp), -- GitLab From a5778bf7ba50e3c04f4c101dc1ccd5ca1585aefa Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 14:24:11 +0100 Subject: [PATCH 125/992] Fixed BLAS library flags style issue --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index 25b2a7b0a9..ca0386a404 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/octave/'] -configopts = ['--with-blas="-lopenblas"'] +configopts = ['--with-blas="${LIBBLAS}"'] dependencies = [ ('PCRE', '8.36'), -- GitLab From 5f37d6f259c244941c2c388fd4a543bf077052f7 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 15:28:41 +0100 Subject: [PATCH 126/992] Fixed some more style issues --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index ca0386a404..e311f5fe2d 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -6,10 +6,10 @@ description = """GNU Octave is a high-level interpreted language, primarily inte toolchain = {'name': 'foss', 'version': '2015a'} -sources = [SOURCELOWER_TAR_GZ] +sources = [GNU_SOURCE] source_urls = ['http://ftpmirror.gnu.org/octave/'] -configopts = ['--with-blas="${LIBBLAS}"'] +configopts = '--with-blas="${LIBBLAS}"' dependencies = [ ('PCRE', '8.36'), -- GitLab From c6a3e90a717bc1766ccf7b314c7fc5e72a8683d0 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 14:38:40 +0100 Subject: [PATCH 127/992] Added foss easyconfig for libffi --- .../l/libffi/libffi-3.2.1-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb new file mode 100644 index 0000000000..17a9f263e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 7ebc21cd01ea2cafb635489e1c3596490725f174 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 14:47:27 +0100 Subject: [PATCH 128/992] Added foss easyconfig for gettext --- .../g/gettext/gettext-0.19.4-foss-2015a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb new file mode 100644 index 0000000000..51c244d3ef --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.4' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' -- GitLab From 681107aa60b510d71b2640f4fc1aaf4760d933a9 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 14:49:54 +0100 Subject: [PATCH 129/992] Added foss easyconfig for GLib --- .../g/GLib/GLib-2.42.1-foss-2015a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb new file mode 100644 index 0000000000..167d8fc75b --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.42.1' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.4'), +] +builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' -- GitLab From e1e346e87c0c6ee6c94186aa7ee80a9ebbc6c2d3 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:12:39 +0100 Subject: [PATCH 130/992] Added foss easyconfig for Qt --- .../easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb new file mode 100644 index 0000000000..c226c3cb72 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb @@ -0,0 +1,17 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.42.1')] + +moduleclass = 'devel' -- GitLab From c4cff509183f97b26b3c49e5f45c6f7c83b1694e Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:18:29 +0100 Subject: [PATCH 131/992] Added foss easyconfig for Cube --- .../easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb new file mode 100644 index 0000000000..eac6956fc7 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'EB_Score_minus_P' + +name = "Cube" +version = "4.3" + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] + + +# patches = ['Cube-4.2_fix-Qt-version-check.patch'] + +dependencies = [('Qt', '4.8.6')] + +configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" + +sanity_check_paths = { + 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' -- GitLab From cff53b3ba27ce7f492b01a8dd00856c3c873e436 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:22:20 +0100 Subject: [PATCH 132/992] Added foss easyconfig for OTF2 --- .../o/OTF2/OTF2-1.5.1-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb new file mode 100644 index 0000000000..d09eb89527 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'EB_Score_minus_P' + +name = "OTF2" +version = "1.5.1" + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It will become the new standard trace format + for Scalasca, Vampir, and Tau and is open for other tools.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +sanity_check_paths = { + # note by Bernd Mohr: on some systems libraries end up in lib/ + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 21d27710908a65227ffb63e4026ad8d3a5163557 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:31:29 +0100 Subject: [PATCH 133/992] Added foss easyconfig for OPARI2 --- .../o/OPARI2/OPARI2-1.1.2-foss-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb new file mode 100644 index 0000000000..ad5274512f --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' + +name = "OPARI2" +version = "1.1.2" + +homepage = 'http://www.score-p.org' +description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, + is a source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls to + the POMP2 measurement interface.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +sanity_check_paths = { + 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From dab4edf5dc4a2088ef5c942a722afdb164927946 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:42:49 +0100 Subject: [PATCH 134/992] Added foss easyconfig for PAPI --- .../p/PAPI/PAPI-5.4.0-foss-2015a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb new file mode 100644 index 0000000000..c9ba2ffbaf --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.4.0' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# Example download URL, for reference: http://icl.cs.utk.edu/projects/papi/downloads/papi-5.0.0.tar.gz +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 03995320a28a9c681637feec5b7a274c25bad042 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 15:53:37 +0100 Subject: [PATCH 135/992] Added foss easyconfig for PDT --- .../easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb new file mode 100644 index 0000000000..81d6197602 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -0,0 +1,50 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' + +name = "PDT" +version = "3.20" + +homepage = 'http://www.cs.uoregon.edu/research/pdt/' +description = """Program Database Toolkit (PDT) is a framework for analyzing source + code written in several programming languages and for making rich program knowledge + accessible to developers of static and dynamic analysis tools. PDT implements a standard + program representation, the program database (PDB), that can be accessed in a uniform way + through a class library supporting common PDB operations.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +prefix_opt = '-prefix=' + +# notes by Bernd Mohr +# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect +# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc +configopts = '-GNU' + +keeppreviousinstall = True + +# notes by Bernd Mohr +# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? +sanity_check_paths = { + 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], + 'dirs': [], +} + +skipsteps = ['build'] + +modextrapaths = { + 'PATH': "x86_64/bin", + 'LD_LIBRARY_PATH': "x86_64/lib", +} + +moduleclass = 'perf' -- GitLab From 43ed8d5e7e43a2c116e96329a7b7b5087e6f04df Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 16:07:56 +0100 Subject: [PATCH 136/992] Added foss easyconfig for Score-P --- .../s/Score-P/Score-P-1.4-foss-2015a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb new file mode 100644 index 0000000000..68a27ad6ea --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -0,0 +1,45 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +# make sure we don't fall back to the ConfigureMake easyblock +easyblock = 'EB_Score_minus_P' + +name = 'Score-P' +version = '1.4' + +homepage = 'http://www.score-p.org' +description = """The Score-P measurement infrastructure is a highly scalable and + easy-to-use tool suite for profiling, event tracing, and online analysis of HPC + applications.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz +sources = ["scorep-%(version)s.tar.gz"] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.25', '', ('GCC', '4.9.2')), + ('Cube', '4.3'), + ('OPARI2', '1.1.2'), + ('OTF2', '1.5.1'), + ('PAPI', '5.4.0'), + ('PDT', '3.20'), +] + +maxparallel = 1 + +sanity_check_paths = { + 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", + ("lib64/libscorep_adapter_mpi_event.a", "lib/libscorep_adapter_mpi_event.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 2589d6e9ddc9371fc2ed0ae7301f2638451259e8 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 16:14:29 +0100 Subject: [PATCH 137/992] Added foss easyconfig for Scalasca --- .../s/Scalasca/Scalasca-2.2-foss-2015a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb new file mode 100644 index 0000000000..c088e07420 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'EB_Score_minus_P' + +name = "Scalasca" +version = "2.2" + +homepage = 'http://www.scalasca.org/' +description = """Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The analysis identifies + potential performance bottlenecks -- in particular those concerning communication and + synchronization -- and offers guidance in exploring their causes.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version)s/dist'] + +dependencies = [ + ('Cube', '4.3'), + ('OTF2', '1.5.1'), +] + +sanity_check_paths = { + 'files': ["bin/scalasca", ("lib64/libpearl.replay.a", "lib/libpearl.replay.a")], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 5a9644723c9e2093444c854d563d818bf1004582 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 17:04:09 +0100 Subject: [PATCH 138/992] Removed comment as per request --- easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb index eac6956fc7..55bce806bc 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -20,7 +20,6 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'foss', 'version': '2015a'} -# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] -- GitLab From 3ab998c8b6946b302d44704c52a013dd7eab7ab8 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 17:05:32 +0100 Subject: [PATCH 139/992] Fixed style issues as per request --- easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb index 81d6197602..e261f444df 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -31,6 +31,8 @@ prefix_opt = '-prefix=' # -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc configopts = '-GNU' +skipsteps = ['build'] + keeppreviousinstall = True # notes by Bernd Mohr @@ -40,8 +42,6 @@ sanity_check_paths = { 'dirs': [], } -skipsteps = ['build'] - modextrapaths = { 'PATH': "x86_64/bin", 'LD_LIBRARY_PATH': "x86_64/lib", -- GitLab From a9cfa39894c7c672c3dc34abdc96281ecac2154c Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 6 Feb 2015 14:42:08 +0100 Subject: [PATCH 140/992] scanms easyconfig --- .../SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..76fe9f0898 --- /dev/null +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'PerlModule' + +name = 'SCANMS' +version = '2.02' + +homepage = 'http://compbio.ucmerced.edu/ardell/software/scanms/' +description = """SCANMS is an open source utility written in Perl that works in + conjunction with Richard Hudson’s coalescent simulator MS to do parametric + bootstrapping of a sliding window analysis of neutrality test statistics. + Currently supported statistics are Tajima’s D and Fu and Li’s D* and F*. + Its output of a joint distribution of window minima and maxima may then be + used to correct for multiple comparisons in such analyses.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://compbio.ucmerced.edu/'] +sources = [SOURCELOWER_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +# workaround so sanity check in the PerlModule easyblock works. +# Just check the existence of a perl core module +options = {'modulename': 'POSIX'} + +sanity_check_paths = { + 'files': ["bin/scanms"], + 'dirs': [""] +} + +# copy all the documentation provided in the tarball to install directory +postinstallcmds = ["cp -r %(builddir)s/*/{README,SCANMS.pdf,scanms.doc.html} %(installdir)s"] + +moduleclass = 'bio' -- GitLab From 9ea1a7dedcdd0d2313fc7b50c5e61755605159cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Feb 2015 22:53:06 +0100 Subject: [PATCH 141/992] add easyconfig for bundle of extra R extensions (PoC) --- .../R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb new file mode 100644 index 0000000000..e71e3abf1d --- /dev/null +++ b/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'R-extra' +rver = '3.1.2' +version = '%s-1.0.0' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('GMP', '6.0.0a'), # for gmp +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('gmp', '0.5-12', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' -- GitLab From 32d6b80d049418487f1f5fa325f80c746f2f0ed7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Feb 2015 09:31:12 +0100 Subject: [PATCH 142/992] add easyconfig for JUBE --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb new file mode 100644 index 0000000000..0044a1ec87 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -0,0 +1,22 @@ +easyblock = "VersionIndependentPythonPackage" + +name = "JUBE" +version = "2.0.3" + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ["http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s"] +sources = [SOURCELOWER_TAR_GZ] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 93106b542c5677e5dce0f390969501c2f1d978a3 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 16 Feb 2015 15:28:32 +0100 Subject: [PATCH 143/992] Update download URLs for Qt --- easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb index c226c3cb72..2111ce217a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb @@ -7,8 +7,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'foss', 'version': '2015a'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/', + 'http://master.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -- GitLab From 787816f2e5c7615aecdbae480f33d70a6254f02f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:18:56 +0100 Subject: [PATCH 144/992] Adjusted URL, added checksum, and tweaked build --- .../easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb index 55bce806bc..c0a4d9c729 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -21,18 +21,22 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] - -# patches = ['Cube-4.2_fix-Qt-version-check.patch'] +checksums = [ + 'ed4d6f3647eefa65fc194b5d1a5f4ffe', # cube-4.3.tar.gz +] dependencies = [('Qt', '4.8.6')] -configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" - sanity_check_paths = { 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], 'dirs': ["include/cube", "include/cubew"], } +# If all prerequisites for the Cube Java reader are available on the system, +# parallel builds will fail. Alternatively, disable the Java reader using +# configopts = "--without-java-reader" +maxparallel = 1 + moduleclass = 'perf' -- GitLab From 8af6b22c2d786586ec127d6c3cde869a73e2a52f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:20:08 +0100 Subject: [PATCH 145/992] Added checksum --- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb | 5 ++++- easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb index ad5274512f..6a2ab2df29 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb @@ -19,10 +19,13 @@ description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, toolchain = {'name': 'foss', 'version': '2015a'} -# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +checksums = [ + '9a262c7ca05ff0ab5f7775ae96f3539e', # opari2-1.1.2.tar.gz +] + sanity_check_paths = { 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], 'dirs': [], diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb index d09eb89527..4f583c01b1 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb @@ -18,10 +18,13 @@ description = """The Open Trace Format 2 is a highly scalable, memory efficient toolchain = {'name': 'foss', 'version': '2015a'} -# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +checksums = [ + '16a9df46e0da78e374f5d12c8cdc1109', # otf2-1.5.1.tar.gz +] + sanity_check_paths = { # note by Bernd Mohr: on some systems libraries end up in lib/ 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], -- GitLab From 7807884a30458c3c50b966ddb1ab913a706b27db Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:20:42 +0100 Subject: [PATCH 146/992] Removed outdated comment --- easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb index e261f444df..124698a037 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -20,7 +20,6 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'foss', 'version': '2015a'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -- GitLab From 4e2f20cbf247302abf58968180c92f67daab017f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:21:13 +0100 Subject: [PATCH 147/992] Remved outdated comment, add checksum, and tweaked build --- easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb index 68a27ad6ea..91b0941367 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -20,10 +20,13 @@ description = """The Score-P measurement infrastructure is a highly scalable and toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {"usempi": True} -# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz sources = ["scorep-%(version)s.tar.gz"] source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +checksums = [ + '17bd732cf54097d35157bf0d8284ad78', # scorep-1.4.tar.gz +] + # compiler toolchain depencies dependencies = [ ('binutils', '2.25', '', ('GCC', '4.9.2')), @@ -34,8 +37,6 @@ dependencies = [ ('PDT', '3.20'), ] -maxparallel = 1 - sanity_check_paths = { 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", ("lib64/libscorep_adapter_mpi_event.a", "lib/libscorep_adapter_mpi_event.a")], -- GitLab From c5ac4f05ae2026c706758d3abd32004784c80e14 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 17 Feb 2015 14:25:22 +0100 Subject: [PATCH 148/992] Adjusted URL and added checksum --- easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb index c088e07420..55d127b2f7 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb @@ -21,7 +21,11 @@ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {"usempi": True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version)s/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] + +checksums = [ + '06e0380c612811a1ff9c183fed9331a9', # scalasca-2.2.tar.gz +] dependencies = [ ('Cube', '4.3'), -- GitLab From f1f1bef8d7a3db8bdd0b5340fdfc35c937d25a1c Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 17 Feb 2015 15:55:07 +0100 Subject: [PATCH 149/992] Fixed style issue --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index e311f5fe2d..131eedc724 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'Octave' version = '3.8.2' -- GitLab From c80efece700ec06ab718e2f7c84402dd66b3298b Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 19 Feb 2015 12:47:49 +0100 Subject: [PATCH 150/992] added PeakSeq-1.3-goolf-1.4.10.eb --- .../p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..0a7acf4ed3 --- /dev/null +++ b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = "PeakSeq" +version = "1.3" + +homepage = 'http://info.gersteinlab.org/PeakSeq' +description = """ PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq + experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from + a control experiment and outputs a file with peak regions ranked with increasing Q-values.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/'] +sources = ['%(name)s.zip'] + +# as the tarball doesn't contain the version we verify the checksum to be sure +# we don't download a newer version and consider it as 1.3 +checksums = [('md5', '32b4d71b2ec9455c7db69516b1bd4910')] + +buildopts = ' CC="$CXX"' + +files_to_copy = ["bin", "README" ] + +sanity_check_paths = { + 'files': ["bin/PeakSeq"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 7f0f28e1bf0c6a5bd1ea745a670202fe09246408 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 27 Feb 2015 14:39:05 +0100 Subject: [PATCH 151/992] dummy --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From c1b4a70e085d719044bc78354630bb696d2d81a3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 27 Feb 2015 16:05:47 +0100 Subject: [PATCH 152/992] netCDF and deps foss-2014b --- .../b/Bison/Bison-3.0.2-foss-2014b.eb | 22 +++++++++++++ .../c/CMake/CMake-3.0.0-foss-2014b.eb | 22 +++++++++++++ .../c/cURL/cURL-7.37.1-foss-2014b.eb | 27 ++++++++++++++++ .../d/Doxygen/Doxygen-1.8.7-foss-2014b.eb | 18 +++++++++++ .../f/flex/flex-2.5.39-foss-2014b.eb | 14 ++++++++ .../h/HDF5/HDF5-1.8.13-foss-2014b.eb | 21 ++++++++++++ .../easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb | 23 +++++++++++++ .../netCDF-C++4-4.2.1-foss-2014b.eb | 24 ++++++++++++++ .../netCDF-Fortran-4.4.0-foss-2014b.eb | 18 +++++++++++ .../n/netCDF/netCDF-4.3.2-foss-2014b.eb | 32 +++++++++++++++++++ .../easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb | 23 +++++++++++++ 11 files changed, 244 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb new file mode 100644 index 0000000000..821e3cc963 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb new file mode 100644 index 0000000000..872f8b4d7d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb new file mode 100644 index 0000000000..00fec4f4d1 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.37.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb new file mode 100644 index 0000000000..9604d1fe3e --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.7' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb new file mode 100644 index 0000000000..6a24b017aa --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb new file mode 100644 index 0000000000..2af8e449bf --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.8.13' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb new file mode 100644 index 0000000000..94ec58056b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb new file mode 100644 index 0000000000..5fcb22ae6f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.2.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] + +dependencies = [('netCDF', '4.3.2')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb new file mode 100644 index 0000000000..4d00f104ad --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.3.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb index e69de29bb2..94c5d118ea 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb @@ -0,0 +1,32 @@ +name = 'netCDF' +version = '4.3.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] + +dependencies = [('HDF5', '1.8.13')] + +builddependencies = [ + ('CMake', '3.0.0'), + ('Doxygen', '1.8.7'), + ('cURL', '7.37.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' + diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb new file mode 100644 index 0000000000..9d1f75c5eb --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 77867574f8ac0fd886564d1d20084236399f519f Mon Sep 17 00:00:00 2001 From: "Balazs Hajgato (hajgato@ulb.ac.be)" Date: Mon, 2 Mar 2015 07:09:33 +0100 Subject: [PATCH 153/992] Use external HDF5 h5(p)cc --- .../n/netCDF/netCDF-4.3.2-foss-2014b.eb | 5 ++++- .../n/netCDF/netCDF-4.3.2-intel-2014b.eb | 5 ++++- .../n/netCDF/netCDF-4.3.2-intel-2015a.eb | 5 ++++- .../n/netCDF/netCDF-4.3.2-parallel-HDF.patch | 21 +++++++++++++++++++ 4 files changed, 33 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb index 94c5d118ea..ffb64828a3 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb index 5ab91b52fe..172783a9aa 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb index bb04604455..0456d513c3 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch new file mode 100644 index 0000000000..d097592f15 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch @@ -0,0 +1,21 @@ +#If a system installed sequential HDF5 exist and we use an external +#parallel HDF5 intsllation then the system installed h5cc will be used +#instead of the external h5pcc. Inspiration from netCDF 4.3.3.1 +#B. Hajgato March 1st 2015 +--- netcdf-4.3.2/CMakeLists.txt.org 2014-04-23 23:35:20.000000000 +0200 ++++ netcdf-4.3.2/CMakeLists.txt 2015-03-01 21:07:55.000000000 +0100 +@@ -637,8 +637,13 @@ + ENDIF(NOT MSVC) + + # Assert HDF5 version. ++ IF(HDF5_IS_PARALLEL) ++ SET(HDF5_CC h5pcc) ++ ELSE() ++ SET(HDF5_CC h5cc) ++ ENDIF() + SET(HDF5_VERSION_REQUIRED 1.8.6) +- execute_process(COMMAND sh -c "h5cc -showconfig | grep -i \"HDF5 version\" | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*$/\\1/'" ++ execute_process(COMMAND sh -c "${HDF5_CC} -showconfig | grep -i \"HDF5 version\" | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*$/\\1/'" + OUTPUT_VARIABLE HDF5_VERSION + ERROR_QUIET + ) -- GitLab From 012458309b9a3b63ac1d5734500ec98c0e6d9c80 Mon Sep 17 00:00:00 2001 From: Nils Christian Date: Wed, 4 Mar 2015 22:31:41 +0100 Subject: [PATCH 154/992] XML::Twig for goolf 1.4.10 --- ...ML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb | 24 +++++++++++++++++++ .../XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb create mode 100644 easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..5248d49efa --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,24 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.41' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('expat', '2.1.0') +] + +options = {'modulename': 'XML::Parser'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..acd24ee883 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,24 @@ +easyblock = 'PerlModule' + +name = 'XML-Twig' +version = '3.48' + +homepage = 'http://search.cpan.org/~mirod/XML-Twig-3.48/' +description = """XML::Twig is (yet another!) XML transformation module.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +source_urls = ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('XML-Parser', '2.41', versionsuffix) +] + +options = {'modulename': 'XML::Twig'} + +moduleclass = 'data' -- GitLab From de9694f5a464b9e3e16145425daa870f7cc8de5b Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 5 Mar 2015 09:27:26 -0500 Subject: [PATCH 155/992] changed to BITBUCKET_SOURCE per note by @wpoely86 --- easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb index a2767dc205..9cca953ebc 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -8,7 +8,7 @@ description = """Eigen is a C++ template library for linear algebra: toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] moduleclass = 'math' -- GitLab From d6df555ece4aa4a319de43d2c851515ca585252a Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Mar 2015 12:01:07 -0500 Subject: [PATCH 156/992] adding the foss-2015a with fpm easyconfig --- .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb new file mode 100644 index 0000000000..f53f7ccb61 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb @@ -0,0 +1,41 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.1.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +sanity_check_paths = { + 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'lib/libruby-static.a', 'lib/libruby.so'], + 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] +} + +configopts = "--disable-install-doc --enable-shared" + +moduleclass = 'lang' + + +exts_list = [ + ('fpm', '1.3.3', { + 'source_tmpl': 'fpm-1.3.3.gem', + 'source_urls': ['http://rubygems.org/downloads/'], + }), + +] -- GitLab From c3c8683809ff1c8bdf8e6cb3c07cd452922d5c7e Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Mar 2015 15:14:34 -0500 Subject: [PATCH 157/992] moving fpm to bundle separate from the base ruby install --- .../Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 31 +++++++++++++++++++ .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 8 ----- 2 files changed, 31 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb new file mode 100644 index 0000000000..e9351e062d --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'Bundle' + +name = 'Ruby-FPM' +rubyver = '2.1.5' +version = '%s-1.0.0' % rubyver + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# these are extensions for Ruby +exts_defaultclass = 'RubyGem' +exts_filter = ("gem list %(ext_name)s -i", "") + +dependencies = [ + ('Ruby', rubyver), +] + +name_tmpl = '%(name)s-%(version)s.gem' +ext_options = { + 'source_urls': [ + 'http://rubygems.org/downloads/', # gem archive + ], + 'source_tmpl': name_tmpl, +} +exts_list = [ + ('fpm', '1.3.3', ext_options), +] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb index f53f7ccb61..c585ab1d31 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb @@ -31,11 +31,3 @@ configopts = "--disable-install-doc --enable-shared" moduleclass = 'lang' - -exts_list = [ - ('fpm', '1.3.3', { - 'source_tmpl': 'fpm-1.3.3.gem', - 'source_urls': ['http://rubygems.org/downloads/'], - }), - -] -- GitLab From 52eed5d1cc5b7a1e5babfb57488ef725532f066f Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Mar 2015 21:42:57 -0500 Subject: [PATCH 158/992] adding dependency gems --- .../r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb index e9351e062d..d664b9bdb3 100644 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb @@ -27,5 +27,11 @@ ext_options = { 'source_tmpl': name_tmpl, } exts_list = [ - ('fpm', '1.3.3', ext_options), + ('fpm', '1.3.3', ext_options), + ('json', '1.8.2', ext_options), + ('cabin', '0.7.1', ext_options), + ('backports', '3.6.4', ext_options), + ('arr-pm', '0.0.9', ext_options), + ('clamp', '0.6.4', ext_options), + ('ffi', '1.9.6', ext_options), ] -- GitLab From 720160c0eb33b58802856a76ba723af6185f00e2 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Mar 2015 21:57:58 -0500 Subject: [PATCH 159/992] missed childprocess dep --- .../easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb index d664b9bdb3..c4f32ff0e9 100644 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb @@ -34,4 +34,5 @@ exts_list = [ ('arr-pm', '0.0.9', ext_options), ('clamp', '0.6.4', ext_options), ('ffi', '1.9.6', ext_options), + ('childprocess', '0.5.5', ext_options), ] -- GitLab From 6f768482ad7e828f631cf3cf98dc6a04e732e5db Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 4 Mar 2015 10:15:32 -0500 Subject: [PATCH 160/992] reorder dependencies to work with local only gem installer --- .../r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb index c4f32ff0e9..1aa58a2ac6 100644 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb @@ -27,12 +27,12 @@ ext_options = { 'source_tmpl': name_tmpl, } exts_list = [ - ('fpm', '1.3.3', ext_options), + ('ffi', '1.9.6', ext_options), + ('childprocess', '0.5.5', ext_options), ('json', '1.8.2', ext_options), ('cabin', '0.7.1', ext_options), ('backports', '3.6.4', ext_options), ('arr-pm', '0.0.9', ext_options), ('clamp', '0.6.4', ext_options), - ('ffi', '1.9.6', ext_options), - ('childprocess', '0.5.5', ext_options), + ('fpm', '1.3.3', ext_options), ] -- GitLab From e7f948cf7bdee92d2d918ea7d3c2195e1b3249b7 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 14 Mar 2015 23:32:33 +0100 Subject: [PATCH 161/992] tophat-2.0.13 and patch --- .../t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb | 36 +++++++++++++++++++ .../t/TopHat/tophat-2.0.13-zlib.patch | 12 +++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb new file mode 100644 index 0000000000..f8a43fe7d6 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.0.13' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = ['tophat-2.0.13-zlib.patch'] + +dependencies = [ + ('Boost', '1.55.0', '-Python-2.7.9'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch new file mode 100644 index 0000000000..278b2edf59 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch @@ -0,0 +1,12 @@ +diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile +--- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 ++++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-03-14 23:21:04.221640935 +0100 +@@ -12,7 +12,7 @@ + PROG= samtools_0.1.18 + INCLUDES= -I. + SUBDIRS= . bcftools +-LIBPATH= ++LIBPATH= -L$(EBROOTZLIB)/lib + LIBCURSES= -lcurses + + .SUFFIXES:.c .o -- GitLab From ebab3de9e7ba5398d007785454f81bb9251f2b07 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 09:53:53 +0100 Subject: [PATCH 162/992] added boost dependency --- .../Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb new file mode 100644 index 0000000000..ce2432d59b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb @@ -0,0 +1,27 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' + -- GitLab From 0c2ba7ec4545445d0ecf5beba4bbaee764dffc63 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 09:55:00 +0100 Subject: [PATCH 163/992] added zlib dependency --- .../z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb new file mode 100644 index 0000000000..57a9f3a015 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + toolchain = {'name': 'goolf', 'version': '1.7.20'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) + toolchainopts = {'optarch': True, 'pic': True} + + sources = [SOURCELOWER_TAR_GZ] + source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +#preconfigopts = 'LDSHARED="$CC -shared"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' + -- GitLab From 44caa0a9e21736c8d56f8ff630b6a8de39347d5f Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 09:59:49 +0100 Subject: [PATCH 164/992] switched to used boost without python --- ....7.20-Python-2.7.9.eb => Boost-1.55.0-goolf-1.7.20.eb} | 8 ++------ .../easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb | 2 +- 2 files changed, 3 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/b/Boost/{Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb => Boost-1.55.0-goolf-1.7.20.eb} (76%) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb similarity index 76% rename from easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb rename to easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index ce2432d59b..269ffc6285 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -10,13 +10,9 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -pythonversion = '2.7.9' -versionsuffix = '-Python-%s' % pythonversion +configopts = '--without-libraries=python' -dependencies = [ - ('bzip2', '1.0.6'), - ('Python', pythonversion), -] +dependencies = [('bzip2', '1.0.6')] # also build boost_mpi boost_mpi = True diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb index f8a43fe7d6..be9db35399 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb @@ -20,7 +20,7 @@ source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = ['tophat-2.0.13-zlib.patch'] dependencies = [ - ('Boost', '1.55.0', '-Python-2.7.9'), + ('Boost', '1.55.0'), ('zlib', '1.2.8'), ] -- GitLab From 2f8b6e3aa86c55c605a51dcbe8cfbf78d626ad1e Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 10:03:28 +0100 Subject: [PATCH 165/992] style fixes zlib easyconfig --- .../easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb index 57a9f3a015..f87254ac39 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -6,14 +6,13 @@ version = '1.2.8' homepage = 'http://www.zlib.net/' description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - toolchain = {'name': 'goolf', 'version': '1.7.20'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) - toolchainopts = {'optarch': True, 'pic': True} + computer hardware and operating system.""" - sources = [SOURCELOWER_TAR_GZ] - source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} -#preconfigopts = 'LDSHARED="$CC -shared"' +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], -- GitLab From 1c8dd2e257ade139800448a9c1a1611d3cf62d83 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 15 Mar 2015 22:01:59 +0100 Subject: [PATCH 166/992] mutect easyconfig --- .../m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb diff --git a/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb new file mode 100644 index 0000000000..ee2805d464 --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'Tarball' + +name = 'muTect' +version = '1.1.4' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +sources = ['%(name)s-%(version)s-bin.zip'] + +java = 'Java' +javaver = '1.7.0_76' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +to execute: java -jar \\$EBROOTMUTECT/%(name)s-%(version)s.jar +""" + +moduleclass = 'bio' -- GitLab From 40f62be55263a83e33f29f37904f9031adc3923c Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:54:38 +0100 Subject: [PATCH 167/992] dropped empty line zlib easyconfig --- easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb index f87254ac39..259095c5c8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -20,4 +20,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -- GitLab From 3ba64da2cf11bf579631b5ff790816026cc56a12 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:55:07 +0100 Subject: [PATCH 168/992] four spaces indent --- easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb index 259095c5c8..f37bbd9742 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -15,8 +15,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], - 'dirs': [], + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], } moduleclass = 'lib' -- GitLab From 61178487b83d54b24718d290126447344aaf7a5a Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:55:36 +0100 Subject: [PATCH 169/992] move parallel=1 above sanity check --- easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb index be9db35399..2a4b09be4d 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb @@ -26,11 +26,11 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST' +parallel = 1 + sanity_check_paths = { 'files': ['bin/tophat'], 'dirs': [], } -parallel = 1 - moduleclass = 'bio' -- GitLab From f42eb31af827ec056d6693d0f6333da1fc9c9c60 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:56:05 +0100 Subject: [PATCH 170/992] dropped empty line boost easyconfig --- easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index 269ffc6285..72d076e794 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -20,4 +20,3 @@ boost_mpi = True osdependencies = [('zlib-devel','zlib1g-dev')] moduleclass = 'devel' - -- GitLab From 07d0e0b3b3e7d9c636d4833202a748ea6e09d53a Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:57:04 +0100 Subject: [PATCH 171/992] style fixes boost easyconfig --- .../easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index 72d076e794..fa03c1c2ae 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -7,16 +7,16 @@ description = """Boost provides free peer-reviewed portable C++ source libraries toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] - -configopts = '--without-libraries=python' +source_urls = [SOURCEFORGE_SOURCE] dependencies = [('bzip2', '1.0.6')] +osdependencies = [('zlib-devel','zlib1g-dev')] + # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +configopts = '--without-libraries=python' moduleclass = 'devel' -- GitLab From 239a018070073f89c3b171b50e709b6531906e38 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 09:58:51 +0100 Subject: [PATCH 172/992] added missing bzip2 dependency --- .../b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb new file mode 100644 index 0000000000..718daa2bc0 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically +compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical +compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.bzip.org/%(version)s/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'tools' -- GitLab From 1b1d525125a974ab20a9bca02a4117cb20d5fb7e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 23 Mar 2015 09:30:47 +0100 Subject: [PATCH 173/992] Dummy --- easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) create mode 100644 easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb new file mode 100644 index 0000000000..421376db9e --- /dev/null +++ b/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb @@ -0,0 +1 @@ +dummy -- GitLab From 680423817c7562b0883fc2809b7cf47ad453aab0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 23 Mar 2015 11:24:07 +0100 Subject: [PATCH 174/992] GLPK 4.55 intel-foss 2015a --- .../g/GLPK/GLPK-4.55-foss-2015a.eb | 28 +++++++++++++++++++ .../g/GLPK/GLPK-4.55-intel-2015a.eb | 28 +++++++++++++++++++ .../g/gplk/GPLK-4.55-intel-2015a.eb | 1 - 3 files changed, 56 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb new file mode 100644 index 0000000000..00491cc9ba --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.55' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.0.0a')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb new file mode 100644 index 0000000000..77009b52a1 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.55' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.0.0a')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb deleted file mode 100644 index 421376db9e..0000000000 --- a/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb +++ /dev/null @@ -1 +0,0 @@ -dummy -- GitLab From c696dbe4d68d5d2fafd6c2547caa5c9bbf33e281 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 24 Mar 2015 16:47:08 +0100 Subject: [PATCH 175/992] Create BuildEnv-1.0-intel-2015a-default.eb Add an easyconfig for the BuildEnv easyblock --- .../b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb new file mode 100644 index 0000000000..7c00f91195 --- /dev/null +++ b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb @@ -0,0 +1,13 @@ +easyblock = "BuildEnv" + +name = 'BuildEnv' +version = '1.0' +versionsuffix = '-default' + + +homepage = 'None' +description = """This module sets a set of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +moduleclass = 'devel' -- GitLab From afb53d7ffad5c88ee04c60c75d81c2988494754c Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 08:18:44 +0100 Subject: [PATCH 176/992] Update BuildEnv-1.0-intel-2015a-default.eb --- .../b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb index 7c00f91195..93fc3fedab 100644 --- a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb +++ b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb @@ -4,9 +4,10 @@ name = 'BuildEnv' version = '1.0' versionsuffix = '-default' - homepage = 'None' -description = """This module sets a set of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software.""" +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you + can use to easily transition between toolchains when building your software. To query the variables being set please use: + module show """ toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From 7e72cb4dabf6ba7af5e2d448647458eb3fbdba86 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 10:52:08 +0100 Subject: [PATCH 177/992] Update BuildEnv-1.0-intel-2015a-default.eb --- .../easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb index 93fc3fedab..e3707468df 100644 --- a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb +++ b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb @@ -2,7 +2,6 @@ easyblock = "BuildEnv" name = 'BuildEnv' version = '1.0' -versionsuffix = '-default' homepage = 'None' description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you -- GitLab From 8f6c9de75ba19f8edf52f692dcc07f6f48dcca0f Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 12:42:24 +0100 Subject: [PATCH 178/992] Update BuildEnv-1.0-intel-2015a-default.eb ```default``` is not allowed by lmod so had to use ```defaults``` --- .../easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb index e3707468df..7e91b365f2 100644 --- a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb +++ b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb @@ -1,7 +1,7 @@ easyblock = "BuildEnv" name = 'BuildEnv' -version = '1.0' +version = 'defaults' homepage = 'None' description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you -- GitLab From 5bbbbf1169ff2bab36eee2d690d24584d0561e55 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 12:54:46 +0100 Subject: [PATCH 179/992] Rename BuildEnv-1.0-intel-2015a-default.eb to BuildEnv-defaults-intel-2015a-default.eb --- ...-2015a-default.eb => BuildEnv-defaults-intel-2015a-default.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/BuildEnv/{BuildEnv-1.0-intel-2015a-default.eb => BuildEnv-defaults-intel-2015a-default.eb} (100%) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a-default.eb similarity index 100% rename from easybuild/easyconfigs/b/BuildEnv/BuildEnv-1.0-intel-2015a-default.eb rename to easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a-default.eb -- GitLab From e33c0ceb779e8d4fa1315f583e0b0dfc7d3bc526 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 25 Mar 2015 12:55:05 +0100 Subject: [PATCH 180/992] Rename BuildEnv-defaults-intel-2015a-default.eb to BuildEnv-defaults-intel-2015a.eb --- ...ts-intel-2015a-default.eb => BuildEnv-defaults-intel-2015a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/BuildEnv/{BuildEnv-defaults-intel-2015a-default.eb => BuildEnv-defaults-intel-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a-default.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a-default.eb rename to easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb -- GitLab From 2e566d1576409d4a1d1f81cbad8be150904e8073 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Mar 2015 10:19:04 +0100 Subject: [PATCH 181/992] {numlib}[intel/2015a] PETSc/SLEPc 3.5.3 --- .../c/CMake/CMake-3.2.1-intel-2015a.eb | 22 ++++++++++++++ .../h/Hypre/Hypre-2.10.0b-intel-2015a.eb | 22 ++++++++++++++ .../m/METIS/METIS-5.1.0-intel-2015a.eb | 22 ++++++++++++++ .../PETSc-3.5.3-intel-2015a-Python-2.7.9.eb | 30 +++++++++++++++++++ .../SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb | 19 ++++++++++++ 5 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb new file mode 100644 index 0000000000..4982739fa2 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb new file mode 100644 index 0000000000..160c06dcb8 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb @@ -0,0 +1,22 @@ +name = 'Hypre' +version = '2.10.0b' + +homepage = "https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html" +description = """Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. + The problems of interest arise in the simulation codes being developed at LLNL and elsewhere + to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +# download via https://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b_reg.php +sources = [SOURCELOWER_TAR_GZ] + +start_dir = "src" + +sanity_check_paths = { + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb new file mode 100644 index 0000000000..ef2bf9ff97 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb @@ -0,0 +1,22 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +patches = ['METIS_IDXTYPEWIDTH.patch'] + +builddependencies = [('CMake', '3.0.0')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..6f526fc72b --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,30 @@ +name = 'PETSc' +version = '3.5.3' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['PETSc_ranlib-fix.patch'] + +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +dependencies = [ + ('Boost', '1.57.0', versionsuffix), + ('METIS', '5.1.0'), + (parmetis, parmetis_ver), + ('SCOTCH', '6.0.4'), + ('SuiteSparse', '4.4.3', '-%s-%s' % (parmetis, parmetis_ver)), + ('Hypre', '2.10.0b'), +] + +builddependencies = [('CMake', '3.2.1')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..2253b31148 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'SLEPc' +version = '3.5.3' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.grycap.upv.es/slepc/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of + large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either + standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial + SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.grycap.upv.es/slepc/download/download.php?filename='] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('PETSc', '3.5.3', versionsuffix)] + +moduleclass = 'numlib' -- GitLab From e67c6f672ebcdbccbc1c869bfb4ef7c1a0095d6f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Mar 2015 15:25:27 +0100 Subject: [PATCH 182/992] reinclude FIAT and ScientificPython (that depends on an older numpy) as PETSc deps --- .../FIAT-1.5.0-intel-2015a-Python-2.7.9.eb | 35 ++++++++++++++++++ .../PETSc-3.5.3-intel-2015a-Python-2.7.9.eb | 2 ++ ...icPython-2.9.4-intel-2015a-Python-2.7.9.eb | 36 +++++++++++++++++++ 3 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..03fe5cf7a1 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.5.0' + +homepage = 'ttps://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order +instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating +arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('ScientificPython', '2.9.4', versionsuffix), + ('sympy', '0.7.6', versionsuffix), +] + +options = {'modulename': name} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/FIAT' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb index 6f526fc72b..4842cf5227 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -18,8 +18,10 @@ parmetis = 'ParMETIS' parmetis_ver = '4.0.3' dependencies = [ ('Boost', '1.57.0', versionsuffix), + ('FIAT', '1.5.0', versionsuffix), ('METIS', '5.1.0'), (parmetis, parmetis_ver), + ('ScientificPython', '2.9.4', versionsuffix), ('SCOTCH', '6.0.4'), ('SuiteSparse', '4.4.3', '-%s-%s' % (parmetis, parmetis_ver)), ('Hypre', '2.10.0b'), diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..0170615e9c --- /dev/null +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'ScientificPython' +version = '2.9.4' + +homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' +description = """ScientificPython is a collection of Python modules for scientific computing. + It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, + and parallelization.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + # older version of numpy than the one included in Python module required + # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for + ('numpy', '1.8.2', versionsuffix), +] + +options = {'modulename': 'Scientific'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Scientific' % pythonshortversion], +} + +moduleclass = 'math' -- GitLab From bb78d65b3db5a14742bed3f7de4e8352598b0981 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Mar 2015 15:26:20 +0100 Subject: [PATCH 183/992] add missing sympy/numpy easyconfigs --- .../easyconfigs/n/numpy/numpy-1.8.1-mkl.patch | 213 ++++++++++++++++++ .../numpy-1.8.2-intel-2015a-Python-2.7.9.eb | 26 +++ .../sympy-0.7.6-intel-2015a-Python-2.7.9.eb | 32 +++ 3 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch new file mode 100644 index 0000000000..363f95c19f --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch @@ -0,0 +1,213 @@ +diff -ur numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py +--- numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py 2014-03-25 20:43:24.000000000 +0100 ++++ numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py 2014-07-08 15:22:31.471064031 +0200 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ur numpy-1.8.1.orig/numpy/distutils/system_info.py numpy-1.8.1-2/numpy/distutils/system_info.py +--- numpy-1.8.1.orig/numpy/distutils/system_info.py 2014-03-25 20:43:24.000000000 +0100 ++++ numpy-1.8.1-2/numpy/distutils/system_info.py 2014-07-08 15:32:34.480063940 +0200 +@@ -600,7 +600,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + return self.get_libs(key, '') +@@ -642,6 +642,23 @@ + lib_dirs) + return info + ++ def check_libs_all(self,lib_dir,libs,opt_libs =[]): ++ """If static or shared libraries are available then return ++ their info dictionary. ++ ++ Checks for all libraries as shared libraries first, then ++ static (or vice versa if self.search_static_first is True). ++ """ ++ exts = self.library_extensions() ++ info = None ++ for ext in exts: ++ info = self._check_libs_all(lib_dir,libs,opt_libs,[ext]) ++ if info is not None: ++ break ++ if not info: ++ log.info(' libraries %s not found in %s', ','.join(libs), lib_dir) ++ return info ++ + def check_libs2(self, lib_dirs, libs, opt_libs=[]): + """If static or shared libraries are available then return + their info dictionary. +@@ -655,6 +672,18 @@ + lib_dirs) + return info + ++ def check_libs2_all(self, lib_dirs, libs, opt_libs =[]): ++ """If static or shared libraries are available then return ++ their info dictionary. ++ ++ Checks each library for shared or static. ++ """ ++ exts = self.library_extensions() ++ info = self._check_libs_all(lib_dirs,libs,opt_libs,exts) ++ if not info: ++ log.info(' libraries %s not found in %s', ','.join(libs), os.pathsep.join(lib_dirs)) ++ return info ++ + def _lib_list(self, lib_dir, libs, exts): + assert is_string(lib_dir) + liblist = [] +@@ -665,6 +694,9 @@ + lib_prefixes = ['lib'] + # for each library name, see if we can find a file for it. + for l in libs: ++ if l[0]=='-': ++ liblist.append(l) ++ continue + for ext in exts: + for prefix in lib_prefixes: + p = self.combine_paths(lib_dir, prefix + l + ext) +@@ -680,6 +712,19 @@ + break + return liblist + ++ def _lib_list_all(self, lib_dirs, libs, exts): ++ assert (type(lib_dirs)==list) ++ if lib_dirs: ++ assert is_string(lib_dirs[0]) ++ liblist=[] ++ for lib_dir in lib_dirs: ++ ls=self._lib_list(lib_dir,libs,exts) ++ for l in ls: ++ log.info("(_lib_list_all) Found %s in %s"%(l,lib_dir)) ++ if l not in liblist: ++ liblist.append(l) ++ return liblist ++ + def _check_libs(self, lib_dirs, libs, opt_libs, exts): + """Find mandatory and optional libs in expected paths. + +@@ -721,6 +766,22 @@ + else: + return None + ++ def _check_libs_all(self, lib_dirs, libs, opt_libs, exts): ++ found_libs_unordered = self._lib_list_all(lib_dirs, libs, exts) ++ # ensure same order as in lib_dirs ++ found_libs = [] ++ for lib_dir in libs: ++ if lib_dir in found_libs_unordered: ++ found_libs.append(lib_dir) ++ if len(found_libs) == len(libs): ++ info = {'libraries' : found_libs, 'library_dirs' : lib_dirs} ++ opt_found_libs = self._lib_list_all(lib_dirs, opt_libs, exts) ++ if len(opt_found_libs) == len(opt_libs): ++ info['libraries'].extend(opt_found_libs) ++ return info ++ else: ++ return ++ + def combine_paths(self, *args): + """Return a list of existing paths composed by all combinations + of items from the arguments. +@@ -953,9 +1014,11 @@ + lib_dirs = self.get_lib_dirs() + incl_dirs = self.get_include_dirs() + mkl_libs = self.get_libs('mkl_libs', self._lib_mkl) +- info = self.check_libs2(lib_dirs, mkl_libs) +- if info is None: ++ mkl = None ++ mkl = self.check_libs2_all(lib_dirs,mkl_libs) ++ if mkl is None: + return ++ info = mkl + dict_append(info, + define_macros=[('SCIPY_MKL_H', None)], + include_dirs=incl_dirs) +@@ -1017,16 +1080,13 @@ + atlas = None + lapack = None + atlas_1 = None +- for d in lib_dirs: +- atlas = self.check_libs2(d, atlas_libs, []) +- lapack_atlas = self.check_libs2(d, ['lapack_atlas'], []) +- if atlas is not None: +- lib_dirs2 = [d] + self.combine_paths(d, ['atlas*', 'ATLAS*']) +- lapack = self.check_libs2(lib_dirs2, lapack_libs, []) +- if lapack is not None: +- break +- if atlas: +- atlas_1 = atlas ++ atlas = self.check_libs2_all(lib_dirs, atlas_libs) ++ lapack_atlas = self.check_libs2_all(lib_dirs, ['lapack_atlas']) ++ if atlas is not None: ++ lib_dirs2 = lib_dirs + self.combine_paths(lib_dirs,['atlas*','ATLAS*']) ++ lapack = self.check_libs2_all(lib_dirs2, lapack_libs) ++ if atlas: ++ atlas_1 = atlas + log.info(self.__class__) + if atlas is None: + atlas = atlas_1 +@@ -1105,7 +1165,8 @@ + info = {} + atlas_libs = self.get_libs('atlas_libs', + self._lib_names + self._lib_atlas) +- atlas = self.check_libs2(lib_dirs, atlas_libs, []) ++ atlas = None ++ atlas = self.check_libs2_all(lib_dirs, atlas_libs) + if atlas is None: + return + include_dirs = self.get_include_dirs() +@@ -1153,8 +1214,10 @@ + lib_dirs = self.get_lib_dirs() + + lapack_libs = self.get_libs('lapack_libs', self._lib_names) +- info = self.check_libs(lib_dirs, lapack_libs, []) +- if info is None: ++ lapack = self.check_libs_all(lib_dirs, lapack_libs, []) ++ if lapack is not None: ++ info = lapack ++ else: + return + info['language'] = 'f77' + self.set_info(**info) +@@ -1548,8 +1611,10 @@ + lib_dirs = self.get_lib_dirs() + + blas_libs = self.get_libs('blas_libs', self._lib_names) +- info = self.check_libs(lib_dirs, blas_libs, []) +- if info is None: ++ blas = self.check_libs_all(lib_dirs, blas_libs, []) ++ if blas is not None: ++ info = blas ++ else: + return + info['language'] = 'f77' # XXX: is it generally true? + self.set_info(**info) +diff -ur numpy-1.8.1.orig/numpy/distutils/unixccompiler.py numpy-1.8.1-2/numpy/distutils/unixccompiler.py +--- numpy-1.8.1.orig/numpy/distutils/unixccompiler.py 2014-03-25 20:43:23.000000000 +0100 ++++ numpy-1.8.1-2/numpy/distutils/unixccompiler.py 2014-07-08 15:34:01.924063926 +0200 +@@ -111,3 +111,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..db3bc90ff5 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.8.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.1-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..4722866acf --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'sympy' +version = '0.7.6' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/sympy/sympy/releases/download/sympy-%(version)s/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sympy' % pythonshortversion], +} + +moduleclass = 'math' -- GitLab From 94b31baab93d43b55ee13dab50729911dcc0e85a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Mar 2015 15:27:23 +0100 Subject: [PATCH 184/992] add easyconfigs for gmsh and getdp --- .../g/getdp/getdp-2.5.0-intel-2015a.eb | 24 +++++++++++++++++++ .../g/gmsh/gmsh-2.9.1-intel-2015a.eb | 23 ++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb new file mode 100644 index 0000000000..1a8738bd04 --- /dev/null +++ b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'getdp' +version = '2.5.0' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://geuz.org/getdp' +description = """GetDP is an open source finite element solver using mixed elements to discretize de Rham-type + complexes in one, two and three dimensions.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geuz.org/getdp/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] + +dependencies = [ + ('GSL', '1.16'), + ('PETSc', '3.5.3', versionsuffix), + ('SLEPc', '3.5.3', versionsuffix), +] + +separate_build_dir = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb new file mode 100644 index 0000000000..00701f2eb2 --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '2.9.1' + +homepage = 'http://geuz.org/gmsh' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geuz.org/gmsh/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] + +separate_build_dir = True + +configopts = '-DENABLE_FLTK=0' + +sanity_check_paths = { + 'files': ['bin/gmsh'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From c53159e9b1f6e748446c586a61d452b1256708d0 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Fri, 27 Mar 2015 21:33:13 -0400 Subject: [PATCH 185/992] adding a couple of dummy versions --- .../r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb | 38 +++++++++++++++++++ easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 33 ++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb new file mode 100644 index 0000000000..065470ac86 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Bundle' + +name = 'Ruby-FPM' +rubyver = '2.1.5' +version = '%s-1.0.0' % rubyver + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# these are extensions for Ruby +exts_defaultclass = 'RubyGem' +exts_filter = ("gem list %(ext_name)s -i", "") + +dependencies = [ + ('Ruby', rubyver), +] + +name_tmpl = '%(name)s-%(version)s.gem' +ext_options = { + 'source_urls': [ + 'http://rubygems.org/downloads/', # gem archive + ], + 'source_tmpl': name_tmpl, +} +exts_list = [ + ('ffi', '1.9.6', ext_options), + ('childprocess', '0.5.5', ext_options), + ('json', '1.8.2', ext_options), + ('cabin', '0.7.1', ext_options), + ('backports', '3.6.4', ext_options), + ('arr-pm', '0.0.9', ext_options), + ('clamp', '0.6.4', ext_options), + ('fpm', '1.3.3', ext_options), +] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb new file mode 100644 index 0000000000..cce8d3ff7e --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -0,0 +1,33 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.1.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +sanity_check_paths = { + 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'lib/libruby-static.a', 'lib/libruby.so'], + 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] +} + +configopts = "--disable-install-doc --enable-shared" + +moduleclass = 'lang' + -- GitLab From d31e2766fa8c2ddce8d0102126ed46833424ba8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Mar 2015 12:59:48 +0200 Subject: [PATCH 186/992] add easyconfig for extra R extensions that require additional dependencies --- .../c/cURL/cURL-7.41.0-intel-2015a.eb | 30 ++++++ .../o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 24 +++++ .../R-extra-20150323-intel-2015a-R-3.1.3.eb | 99 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 +++++ .../easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb | 24 +++++ 5 files changed, 202 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb create mode 100644 easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb new file mode 100644 index 0000000000..7c9526c34b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.41.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# dependencies = [('OpenSSL', '1.0.1m')] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# configopts = "--with-ssl=$EBROOTOPENSSL" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb new file mode 100644 index 0000000000..ba650f6541 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1m' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb new file mode 100644 index 0000000000..7ec2e95168 --- /dev/null +++ b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb @@ -0,0 +1,99 @@ +easyblock = 'Bundle' + +name = 'R-extra' +version = '20150323' +rver = '3.1.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('Tcl', '8.6.4'), + ('Tk', '8.6.4'), + ('cURL', '7.41.0'), + ('libxml2', '2.9.2'), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('RCurl', '1.95-4.5', ext_options), # requires cURL + ('XML', '3.98-1.1', ext_options), # requires libxml2 + # extensions below requires one or more extensions that have an external dependency listed above + ('picante', '1.6-2', ext_options), + ('spacodiR', '0.13.0115', ext_options), + ('picante', '1.6-2', ext_options), + ('httr', '0.6.1', ext_options), + ('tkWidgets', '1.44.0', bioconductor_options), + ('Mfuzz', '2.26.0', bioconductor_options), + ('maSigPro', '1.38.0', bioconductor_options), + ('rtracklayer', '1.26.2', bioconductor_options), + ('BSgenome', '1.34.1', bioconductor_options), + ('GEOquery', '2.32.0', bioconductor_options), + ('biomaRt', '2.22.0', bioconductor_options), + ('annotate', '1.44.0', bioconductor_options), + ('GSEABase', '1.28.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('Category', '2.32.0', bioconductor_options), + ('GOstats', '2.32.0', bioconductor_options), + ('geneplotter', '1.44.0', bioconductor_options), + ('DESeq2', '1.6.3', bioconductor_options), + ('GenomicFeatures', '1.18.4', bioconductor_options), + ('VariantAnnotation', '1.12.9', bioconductor_options), + ('biovizBase', '1.14.1', bioconductor_options), + ('OrganismDbi', '1.8.1', bioconductor_options), + ('ggbio', '1.14.0', bioconductor_options), + ('ReportingTools', '2.6.0', bioconductor_options), + ('affycoretools', '1.38.0', bioconductor_options), + ('AgiMicroRna', '2.16.0', bioconductor_options), + ('DESeq', '1.18.0', bioconductor_options), + ('GenomeGraphs', '1.26.0', bioconductor_options), + ('geneLenDataBase', '1.1.1', bioconductor_options), + ('goseq', '1.18.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.0.0', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('KEGGgraph', '1.24.0', bioconductor_options), + ('KEGGREST', '1.6.4', bioconductor_options), + ('KEGGprofile', '1.8.0', bioconductor_options), + ('minfi', '1.12.0', bioconductor_options), + ('methylumi', '2.12.0', bioconductor_options), + ('lumi', '2.18.0', bioconductor_options), + ('Gviz', '1.10.10', bioconductor_options), + ('methyAnalysis', '1.8.0', bioconductor_options), + ('pathview', '1.6.0', bioconductor_options), + ('SPIA', '2.18.0', bioconductor_options), + ('cummeRbund', '2.8.2', bioconductor_options), + ('spliceR', '1.8.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..b2673863fd --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..de684154a7 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From eccd8d37c184e95ffaefd240d0f707d0cbeb4b69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 12:11:50 +0200 Subject: [PATCH 187/992] {vis}[intel/2015a] motif 2.3.4 with libX11 1.6.3 (REVIEW) --- .../l/libICE/libICE-1.0.9-intel-2015a.eb | 27 +++++++++++ .../l/libSM/libSM-1.2.2-intel-2015a.eb | 28 +++++++++++ .../libXt-1.1.4-intel-2015a-libX11-1.6.3.eb | 41 ++++++++++++++++ .../motif-2.3.4-intel-2015a-libX11-1.6.3.eb | 47 +++++++++++++++++++ .../x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb | 19 ++++++++ 5 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb new file mode 100644 index 0000000000..57f6a9f4e3 --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xtrans', '1.3.5'), +] + +builddependencies = [ + ('xproto', '7.0.27'), +] + +sanity_check_paths = { + 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb new file mode 100644 index 0000000000..7d8fcfe61a --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libSM' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Session Management library, which allows for applications to both manage sessions, + and make use of session managers to save and restore their state for later use.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libICE', '1.0.9'), +] +builddependencies = [ + ('xproto', '7.0.27'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs' : [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000..507c378340 --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libXt' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are + based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver +dependencies = [ + ('libSM', '1.2.2'), + ('libICE', '1.0.9'), + ('libX11', libx11ver, '-Python-2.7.9'), +] + +builddependencies = [ + ('xproto', '7.0.27'), + ('kbproto', '1.0.6'), +] + +sanity_check_paths = { + 'files' : ['include/X11/%s' % x for x in [ + 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', + 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', + 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', + 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', + 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', + ] + ], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000..af0e37ef27 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.4' + +homepage = 'http://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s-%(version)s-src.tgz'] +source_urls = [SOURCEFORGE_SOURCE] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver +dependencies = [ + ('libXt', '1.1.4', versionsuffix), + ('libXau', '1.0.8'), + ('libX11', libx11ver, '-Python-2.7.9'), + ('libXext', '1.3.3'), + ('libXdmcp', '1.1.2'), + ('libpng', '1.6.16'), + ('xbitmaps', '1.1.1'), + ('freetype', '2.5.5'), + ('libjpeg-turbo', '1.4.0'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('libtool', '2.4.5', '', ('GCC', '4.9.2')), + ('flex', '2.5.39', '', ('GCC', '4.9.2')), + ('Bison', '3.0.4', '', ('GCC', '4.9.2')), + ('util-linux', '2.26.1'), +] + +preconfigopts = "./autogen.sh && " + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb new file mode 100644 index 0000000000..159e636639 --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xbitmaps' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """provides bitmaps for x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] + +sanity_check_paths = { + 'files' : ['include/X11/bitmaps/gray'], + 'dirs' : [] +} + +moduleclass = 'devel' -- GitLab From 90f82fc33c672da56907eac2fa780afb122b077e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 12:37:01 +0200 Subject: [PATCH 188/992] include Autotools as build dep, rather than only libtool --- .../easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb index af0e37ef27..e2cf7a0446 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb @@ -28,7 +28,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] builddependencies = [ - ('libtool', '2.4.5', '', ('GCC', '4.9.2')), + ('Autotools', '20150119', '', ('GCC', '4.9.2')), ('flex', '2.5.39', '', ('GCC', '4.9.2')), ('Bison', '3.0.4', '', ('GCC', '4.9.2')), ('util-linux', '2.26.1'), -- GitLab From 7bbe28c2ab6f98dd788b27abf735222961966954 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 13:09:32 +0200 Subject: [PATCH 189/992] enable lowopt for motif with intel/2015a to dance around compiler segfault --- .../easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb index e2cf7a0446..3197280c43 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb @@ -9,6 +9,8 @@ description = """Motif refers to both a graphical user interface (GUI) specifica It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" toolchain = {'name': 'intel', 'version': '2015a'} +# use -O1 to dance around icc segfaulting +toolchainopts = {'lowopt': True} sources = ['%(name)s-%(version)s-src.tgz'] source_urls = [SOURCEFORGE_SOURCE] -- GitLab From 243d569d112dda1ce81227797bd8dee8f9a11746 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Fri, 27 Mar 2015 16:27:48 +0100 Subject: [PATCH 190/992] Support for hanythingondemand. --- ...ondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 35 +++++++++++++++++++ ...netaddr-0.7.13-intel-2015a-Python-2.7.9.eb | 24 +++++++++++++ ...tifaces-0.10.4-intel-2015a-Python-2.7.9.eb | 26 ++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..caad6b3b27 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '2.2.0' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +installopts='--single-version-externally-managed --record=record' + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.3.5', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '1.9.1', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.13', versionsuffix), +] + +options = {'modulename': 'hod'} + diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..b1bffb16b3 --- /dev/null +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'netaddr' +version = '0.7.13' + +homepage = 'https://pypi.python.org/pypi/netaddr' +description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network addresses""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://pypi.python.org/packages/source/n/netaddr/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +options = {'modulename': 'netaddr'} + diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..26d54445b2 --- /dev/null +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'netifaces' +version = '0.10.4' + +homepage = 'https://pypi.python.org/pypi/netifaces' +description = """netifaces provides a (hopefully portable-ish) way for Python +programmers to get access to a list of the network interfaces on the local +machine, and to obtain the addresses of those network interfaces.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://pypi.python.org/packages/source/n/%(namelower)s/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +options = {'modulename': 'netifaces'} + -- GitLab From e5834194ea70de5b46c106e48e8dfdacdc4c0dff Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 30 Mar 2015 16:44:34 +0200 Subject: [PATCH 191/992] Add pbs_python since it wasn't in EB upstream. --- ...s_python-4.3.5-intel-2015a-Python-2.7.9.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..c47f57e15e --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,60 @@ +name = 'pbs_python' +version = '4.3.5' +easyblock = 'ConfigureMake' + +homepage = '' +description = """The pbs_python package is a wrapper class for the Torque Batch System C library. With this package, you + now can write utilities and extensions in Python instead of C. This package was developed to replace xpbsmon by an + ASCII version named pbsmon. PBSQuery is also included in this package. This is a Python module built on top of the pbs + Python module to simplify querying the batch server. There are a lot of examples included in the source package. + """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = [ + 'http://ftp.sara.nl/pub/outgoing/', + 'https://raw.github.com/adaptivecomputing/torque/4.2-dev/src/include/', + 'https://oss.trac.surfsara.nl/pbs_python/raw-attachment/ticket/36/', + ] + +# torque-devel is missing a log.h file we need, so we ship it. +my_startdir = "%s-%s/" % (name, version) + +place_for_include_file = "include/torque" +copy_cmd = 'mkdir -p %s%%s && cp %%%%s %s%%s ' % (my_startdir, my_startdir) +sources = [ + SOURCE_TAR_GZ, + ('log.h', copy_cmd % (place_for_include_file, place_for_include_file)), + ('pbs_wrap_4.2.c', copy_cmd % ('src', 'src')), +] +patches = [ + 'docdir.patch', + 'setup.py.in_4.2.patch', +] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +osdependencies = ['torque-devel'] +dependencies = [ + (python, pythonver), +] + +# this is needed for setup.py script +preconfigopts = 'export PBS_PYTHON_INCLUDEDIR="$PWD/%s" && ' % place_for_include_file +configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" +prebuildopts = ' %s export CFLAGS="$CFLAGS -I$PWD/%s -I/usr/include/torque/" && ' % (preconfigopts, place_for_include_file) +preinstallopts = prebuildopts + +pythonpath = 'lib/python%s/site-packages/' % pythonshortver +modextrapaths = {"PYTHONPATH": pythonpath} + +sanity_check_paths = { + 'files': [], + 'dirs': ["%spbs" % pythonpath] +} + +moduleclass = 'tools' -- GitLab From 3ec8c9adf9bf3ff6729a9f254be9def38e9a99d5 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 30 Mar 2015 16:49:38 +0200 Subject: [PATCH 192/992] Add patches! --- .../easyconfigs/p/pbs_python/docdir.patch | 12 ++++ .../p/pbs_python/setup.py.in_4.2.patch | 55 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/p/pbs_python/docdir.patch create mode 100644 easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch diff --git a/easybuild/easyconfigs/p/pbs_python/docdir.patch b/easybuild/easyconfigs/p/pbs_python/docdir.patch new file mode 100644 index 0000000000..7c012d8e84 --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/docdir.patch @@ -0,0 +1,12 @@ +--- Makefile.in.orig 2013-11-25 16:19:27.813530658 +0100 ++++ Makefile.in 2013-11-25 16:19:41.980755196 +0100 +@@ -5,7 +5,7 @@ + exec_prefix=$(PREFIX) + BINDIR=$(PREFIX)/bin + +-DOCDIR=/usr/share/doc/pbs-python ++DOCDIR=@docdir@ + EXAMPLES=$(DOCDIR)/examples + + .PHONY: install pythonlib +~ diff --git a/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch b/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch new file mode 100644 index 0000000000..978ba571fd --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch @@ -0,0 +1,55 @@ +diff -uN pbs_python-4.3.5.orig/setup.py.in pbs_python-4.3.5/setup.py.in +--- pbs_python-4.3.5.orig/setup.py.in 2013-12-05 19:49:17.601962399 +0100 ++++ pbs_python-4.3.5/setup.py.in 2013-12-05 19:49:45.713469496 +0100 +@@ -7,8 +7,10 @@ + + import sys + import os ++import glob + +-from distutils.core import setup, Extension ++from distutils.core import setup, Extension ++from distutils.version import LooseVersion + + # Strip off the -L it is also added by the python setup tools + # +@@ -25,13 +27,6 @@ + ### Make symlinks to right torque version + # + VERSION = "@pbs_version@" +-tmp = VERSION.split('.') +- +-major_version = int(tmp[0]) +-minor_version = int(tmp[1]) +-#build_version = int(tmp[2]) +-build_version = int(tmp[2].split('-')[0]) +- + + os.chdir('src') + +@@ -43,7 +38,23 @@ + except OSError: + pass + +-if major_version >= 2 and minor_version >= 4 and build_version >= 7: ++if LooseVersion(VERSION) >= LooseVersion('4.2'): ++ inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') ++ os.environ['CC']=os.environ['CXX'] ++ os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) ++ ++ if not os.path.exists(os.path.join(inc,'log.h')): ++ print 'Failed to find log.h in inlcude dir %s. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable)'%inc ++ sys.exit(2) ++ ++ for fn in glob.glob('*.h'): ++ os.remove(fn) ++ ++ os.symlink('pbs_wrap_4.2.c', 'pbs_wrap.c') ++ os.symlink('pbs_2.4.py', 'pbs.py') ++ ++ TORQUE_VERSION='TORQUE_4_2' ++elif LooseVersion(VERSION) >= LooseVersion('2.4.7'): + os.symlink('pbs_wrap_2.4.c', 'pbs_wrap.c') + os.symlink('pbs_2.4.py', 'pbs.py') + TORQUE_VERSION='TORQUE_2_4' + -- GitLab From 34c9845a27e6d0d1be0bc06158337df19b235e90 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 31 Mar 2015 11:40:11 +0200 Subject: [PATCH 193/992] Add vsc-mympirun and vsc-base files for hanythingondemand. --- .../easyconfigs/v/vsc-base/vsc-base-1.9.1.eb | 19 ++++++++++++++ .../v/vsc-mympirun/vsc-mympirun-3.4.2.eb | 25 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb new file mode 100644 index 0000000000..8fc4fb35d9 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' +name = 'vsc-base' +version = "1.9.1" # tweaked by EasyBuild (was: '1.7.3') + +homepage = 'http://hpcugent.github.com/vsc-mympirun/' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': 'dummy'} + + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'https://github.com/hpcugent/vsc-base/archive/', +] + +options = {'modulename': 'vsc.utils'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb new file mode 100755 index 0000000000..f471f436a3 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb @@ -0,0 +1,25 @@ +easyblock = 'VSCPythonPackage' + +name = 'vsc-mympirun' +version = '3.4.2' + +homepage = 'http://hpcugent.github.com/vsc-mympirun/' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] + +dependencies = [ + ('vsc-base', '1.9.1'), + ('setuptools', '1.4.2'), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +options = {'modulename': 'vsc.mympirun'} + +moduleclass = 'tools' -- GitLab From 7e44e4a88c86c6680629c91baffef7d471f989da Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 31 Mar 2015 14:15:51 +0200 Subject: [PATCH 194/992] Add moduleclass to the .eb files. --- .../hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 1 + .../n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb | 1 + .../n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb index caad6b3b27..fbd087f56f 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -33,3 +33,4 @@ dependencies = [ options = {'modulename': 'hod'} +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb index b1bffb16b3..7a57c70dfb 100644 --- a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb @@ -22,3 +22,4 @@ dependencies = [ options = {'modulename': 'netaddr'} +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb index 26d54445b2..f15deeb6e3 100644 --- a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb @@ -24,3 +24,4 @@ dependencies = [ options = {'modulename': 'netifaces'} +moduleclass = 'tools' -- GitLab From ba2fd41945cd0ed98486d1044ec15daec0e0d491 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Apr 2015 11:55:55 +0200 Subject: [PATCH 195/992] bump netaddr to 0.7.14 --- .../hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 2 +- ...thon-2.7.9.eb => netaddr-0.7.14-intel-2015a-Python-2.7.9.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/netaddr/{netaddr-0.7.13-intel-2015a-Python-2.7.9.eb => netaddr-0.7.14-intel-2015a-Python-2.7.9.eb} (96%) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb index fbd087f56f..c74a578c62 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -28,7 +28,7 @@ dependencies = [ ('vsc-mympirun', '3.4.2', '', True), ('vsc-base', '1.9.1', '', True), ('netifaces', '0.10.4', versionsuffix), - ('netaddr', '0.7.13', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), ] options = {'modulename': 'hod'} diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb similarity index 96% rename from easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb index 7a57c70dfb..e729baad33 100644 --- a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'netaddr' -version = '0.7.13' +version = '0.7.14' homepage = 'https://pypi.python.org/pypi/netaddr' description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network addresses""" -- GitLab From ab061e012414a36e2fe76b4e7d8cc70c8cf5b00c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Apr 2015 11:59:10 +0200 Subject: [PATCH 196/992] fix source URLs for netaddr and netifaces --- .../n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb | 2 +- .../n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb index e729baad33..a12196a3b8 100644 --- a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb @@ -8,7 +8,7 @@ description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://pypi.python.org/packages/source/n/netaddr/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb index f15deeb6e3..26cfac901b 100644 --- a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb @@ -10,7 +10,7 @@ machine, and to obtain the addresses of those network interfaces.""" toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://pypi.python.org/packages/source/n/%(namelower)s/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From ebbacfbdc8ce8b7ef2d03c7e93123fc05b147774 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Apr 2015 12:16:23 +0200 Subject: [PATCH 197/992] bump vsc-base to v2.0.4 --- .../hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 2 +- .../v/vsc-base/{vsc-base-1.9.1.eb => vsc-base-2.0.4.eb} | 8 +++----- .../easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb | 4 ++-- 3 files changed, 6 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/v/vsc-base/{vsc-base-1.9.1.eb => vsc-base-2.0.4.eb} (76%) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb index c74a578c62..6e8188683e 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -26,7 +26,7 @@ dependencies = [ (python, pythonver), ('pbs_python', '4.3.5', versionsuffix), ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '1.9.1', '', True), + ('vsc-base', '2.0.4', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb similarity index 76% rename from easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb rename to easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb index 8fc4fb35d9..24862f2519 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb @@ -1,6 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' + name = 'vsc-base' -version = "1.9.1" # tweaked by EasyBuild (was: '1.7.3') +version = '2.0.4' homepage = 'http://hpcugent.github.com/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" @@ -8,11 +9,8 @@ description = """VSC-tools is a set of Python libraries and scripts that are com # we build this to work with every python version toolchain = {'name': 'dummy', 'version': 'dummy'} - sources = [SOURCE_TAR_GZ] -source_urls = [ - 'https://github.com/hpcugent/vsc-base/archive/', -] +source_urls = [PYPI_SOURCE] options = {'modulename': 'vsc.utils'} diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb index f471f436a3..f1a22d74a6 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb @@ -3,7 +3,7 @@ easyblock = 'VSCPythonPackage' name = 'vsc-mympirun' version = '3.4.2' -homepage = 'http://hpcugent.github.com/vsc-mympirun/' +homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] dependencies = [ - ('vsc-base', '1.9.1'), + ('vsc-base', '2.0.4'), ('setuptools', '1.4.2'), ] -- GitLab From c5cb70531a08c30bca372a3505b5f125d0645fdf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Apr 2015 14:02:22 +0200 Subject: [PATCH 198/992] use most recent pbs_python, use VersionIndependentPythonPackage for HOD --- ...ondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 8 +-- .../easyconfigs/p/pbs_python/docdir.patch | 12 ---- ...s_python-4.3.5-intel-2015a-Python-2.7.9.eb | 60 ------------------- ...s_python-4.6.0-intel-2015a-Python-2.7.9.eb | 41 +++++++++++++ .../p/pbs_python/pbs_python-4.6.0_CC.patch | 20 +++++++ .../p/pbs_python/setup.py.in_4.2.patch | 55 ----------------- 6 files changed, 64 insertions(+), 132 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pbs_python/docdir.patch delete mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch delete mode 100644 easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb index 6e8188683e..581c70ff5f 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'VersionIndependentPythonPackage' name = 'hanythingondemand' version = '2.2.0' @@ -16,15 +16,13 @@ sources = ['%s.tar.gz' % version] python = 'Python' pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pythonshortver = '.'.join(pythonver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonver) -installopts='--single-version-externally-managed --record=record' - # a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime dependencies = [ (python, pythonver), - ('pbs_python', '4.3.5', versionsuffix), + ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', '', True), ('vsc-base', '2.0.4', '', True), ('netifaces', '0.10.4', versionsuffix), diff --git a/easybuild/easyconfigs/p/pbs_python/docdir.patch b/easybuild/easyconfigs/p/pbs_python/docdir.patch deleted file mode 100644 index 7c012d8e84..0000000000 --- a/easybuild/easyconfigs/p/pbs_python/docdir.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- Makefile.in.orig 2013-11-25 16:19:27.813530658 +0100 -+++ Makefile.in 2013-11-25 16:19:41.980755196 +0100 -@@ -5,7 +5,7 @@ - exec_prefix=$(PREFIX) - BINDIR=$(PREFIX)/bin - --DOCDIR=/usr/share/doc/pbs-python -+DOCDIR=@docdir@ - EXAMPLES=$(DOCDIR)/examples - - .PHONY: install pythonlib -~ diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb deleted file mode 100644 index c47f57e15e..0000000000 --- a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb +++ /dev/null @@ -1,60 +0,0 @@ -name = 'pbs_python' -version = '4.3.5' -easyblock = 'ConfigureMake' - -homepage = '' -description = """The pbs_python package is a wrapper class for the Torque Batch System C library. With this package, you - now can write utilities and extensions in Python instead of C. This package was developed to replace xpbsmon by an - ASCII version named pbsmon. PBSQuery is also included in this package. This is a Python module built on top of the pbs - Python module to simplify querying the batch server. There are a lot of examples included in the source package. - """ - -toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'usempi': True} - -source_urls = [ - 'http://ftp.sara.nl/pub/outgoing/', - 'https://raw.github.com/adaptivecomputing/torque/4.2-dev/src/include/', - 'https://oss.trac.surfsara.nl/pbs_python/raw-attachment/ticket/36/', - ] - -# torque-devel is missing a log.h file we need, so we ship it. -my_startdir = "%s-%s/" % (name, version) - -place_for_include_file = "include/torque" -copy_cmd = 'mkdir -p %s%%s && cp %%%%s %s%%s ' % (my_startdir, my_startdir) -sources = [ - SOURCE_TAR_GZ, - ('log.h', copy_cmd % (place_for_include_file, place_for_include_file)), - ('pbs_wrap_4.2.c', copy_cmd % ('src', 'src')), -] -patches = [ - 'docdir.patch', - 'setup.py.in_4.2.patch', -] - -python = 'Python' -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) - -osdependencies = ['torque-devel'] -dependencies = [ - (python, pythonver), -] - -# this is needed for setup.py script -preconfigopts = 'export PBS_PYTHON_INCLUDEDIR="$PWD/%s" && ' % place_for_include_file -configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" -prebuildopts = ' %s export CFLAGS="$CFLAGS -I$PWD/%s -I/usr/include/torque/" && ' % (preconfigopts, place_for_include_file) -preinstallopts = prebuildopts - -pythonpath = 'lib/python%s/site-packages/' % pythonshortver -modextrapaths = {"PYTHONPATH": pythonpath} - -sanity_check_paths = { - 'files': [], - 'dirs': ["%spbs" % pythonpath] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..2b1f46d33d --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'pbs_python' +version = '4.6.0' + +homepage = 'https://oss.trac.surfsara.nl/pbs_python' +description = """The pbs_python package is a wrapper class for the Torque C library. With this package you now can + write utilities/extensions in Python instead of C. We developed this package because we want to replace xpbsmon by + an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of + the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.sara.nl/pub/outgoing/'] +sources = [SOURCE_TAR_GZ] + +patches = ['pbs_python-%(version)s_CC.patch'] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +osdependencies = ['torque-devel'] + +# this is needed for setup.py script +configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" +prebuildopts = 'export CFLAGS="$CFLAGS -I/usr/include/torque/" && ' +preinstallopts = prebuildopts + +pythonpath = 'lib/python%s/site-packages' % pythonshortver +modextrapaths = {"PYTHONPATH": pythonpath} + +sanity_check_paths = { + 'files': [], + 'dirs': ["%s/pbs" % pythonpath] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch new file mode 100644 index 0000000000..00d8259263 --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch @@ -0,0 +1,20 @@ +--- pbs_python-4.6.0/setup.py.in.orig 2015-04-01 13:51:18.158956461 +0200 ++++ pbs_python-4.6.0/setup.py.in 2015-04-01 13:52:02.249359723 +0200 +@@ -37,7 +37,7 @@ + if LooseVersion(VERSION) >= LooseVersion('5.0'): + + inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') +- os.environ['CC']='g++' ++ os.environ['CC']= os.environ.get('CXX', 'g++') + os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) + + if not os.path.exists(os.path.join(inc,'log.h')): +@@ -55,7 +55,7 @@ + elif LooseVersion(VERSION) >= LooseVersion('4.2'): + + inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') +- os.environ['CC']='g++' ++ os.environ['CC']= os.environ.get('CXX', 'g++') + os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) + + if not os.path.exists(os.path.join(inc,'log.h')): diff --git a/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch b/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch deleted file mode 100644 index 978ba571fd..0000000000 --- a/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch +++ /dev/null @@ -1,55 +0,0 @@ -diff -uN pbs_python-4.3.5.orig/setup.py.in pbs_python-4.3.5/setup.py.in ---- pbs_python-4.3.5.orig/setup.py.in 2013-12-05 19:49:17.601962399 +0100 -+++ pbs_python-4.3.5/setup.py.in 2013-12-05 19:49:45.713469496 +0100 -@@ -7,8 +7,10 @@ - - import sys - import os -+import glob - --from distutils.core import setup, Extension -+from distutils.core import setup, Extension -+from distutils.version import LooseVersion - - # Strip off the -L it is also added by the python setup tools - # -@@ -25,13 +27,6 @@ - ### Make symlinks to right torque version - # - VERSION = "@pbs_version@" --tmp = VERSION.split('.') -- --major_version = int(tmp[0]) --minor_version = int(tmp[1]) --#build_version = int(tmp[2]) --build_version = int(tmp[2].split('-')[0]) -- - - os.chdir('src') - -@@ -43,7 +38,23 @@ - except OSError: - pass - --if major_version >= 2 and minor_version >= 4 and build_version >= 7: -+if LooseVersion(VERSION) >= LooseVersion('4.2'): -+ inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') -+ os.environ['CC']=os.environ['CXX'] -+ os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) -+ -+ if not os.path.exists(os.path.join(inc,'log.h')): -+ print 'Failed to find log.h in inlcude dir %s. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable)'%inc -+ sys.exit(2) -+ -+ for fn in glob.glob('*.h'): -+ os.remove(fn) -+ -+ os.symlink('pbs_wrap_4.2.c', 'pbs_wrap.c') -+ os.symlink('pbs_2.4.py', 'pbs.py') -+ -+ TORQUE_VERSION='TORQUE_4_2' -+elif LooseVersion(VERSION) >= LooseVersion('2.4.7'): - os.symlink('pbs_wrap_2.4.c', 'pbs_wrap.c') - os.symlink('pbs_2.4.py', 'pbs.py') - TORQUE_VERSION='TORQUE_2_4' - -- GitLab From b7aebb937fd98e5e1cbe5b6ba80ee91e3abd1af3 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 2 Apr 2015 13:50:54 +0200 Subject: [PATCH 199/992] Bump hod and vsc-base for bug fixes. --- ...gondemand-2.2.1-intel-2015a-Python-2.7.9.eb} | 4 ++-- .../easyconfigs/v/vsc-base/vsc-base-2.1.2.eb | 17 +++++++++++++++++ 2 files changed, 19 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/hanythingondemand/{hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb => hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb} (94%) create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb similarity index 94% rename from easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb index 581c70ff5f..241e630c35 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' name = 'hanythingondemand' -version = '2.2.0' +version = '2.2.1' homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. @@ -24,7 +24,7 @@ dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.0.4', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb new file mode 100644 index 0000000000..b0db50051e --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb @@ -0,0 +1,17 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'vsc-base' +version = '2.1.2' + +homepage = 'http://hpcugent.github.com/vsc-mympirun/' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'vsc.utils'} + +moduleclass = 'tools' -- GitLab From f2af4369e6b2f2d212d1ac736d6e943b338b608f Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 2 Apr 2015 14:48:24 +0200 Subject: [PATCH 200/992] Bump vsc-base version. --- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb index f1a22d74a6..e24521bcf5 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] dependencies = [ - ('vsc-base', '2.0.4'), + ('vsc-base', '2.1.2'), ('setuptools', '1.4.2'), ] -- GitLab From a297788484eb778faeef5c9f335a58cc3b33c9b4 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 2 Apr 2015 12:45:56 -0400 Subject: [PATCH 201/992] adding fpm to the dummy Ruby install --- .../Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 38 ------------------- .../r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb | 38 ------------------- easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 19 ++++++++++ 3 files changed, 19 insertions(+), 76 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb delete mode 100644 easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb deleted file mode 100644 index 1aa58a2ac6..0000000000 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'Bundle' - -name = 'Ruby-FPM' -rubyver = '2.1.5' -version = '%s-1.0.0' % rubyver - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -# these are extensions for Ruby -exts_defaultclass = 'RubyGem' -exts_filter = ("gem list %(ext_name)s -i", "") - -dependencies = [ - ('Ruby', rubyver), -] - -name_tmpl = '%(name)s-%(version)s.gem' -ext_options = { - 'source_urls': [ - 'http://rubygems.org/downloads/', # gem archive - ], - 'source_tmpl': name_tmpl, -} -exts_list = [ - ('ffi', '1.9.6', ext_options), - ('childprocess', '0.5.5', ext_options), - ('json', '1.8.2', ext_options), - ('cabin', '0.7.1', ext_options), - ('backports', '3.6.4', ext_options), - ('arr-pm', '0.0.9', ext_options), - ('clamp', '0.6.4', ext_options), - ('fpm', '1.3.3', ext_options), -] diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb deleted file mode 100644 index 065470ac86..0000000000 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'Bundle' - -name = 'Ruby-FPM' -rubyver = '2.1.5' -version = '%s-1.0.0' % rubyver - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# these are extensions for Ruby -exts_defaultclass = 'RubyGem' -exts_filter = ("gem list %(ext_name)s -i", "") - -dependencies = [ - ('Ruby', rubyver), -] - -name_tmpl = '%(name)s-%(version)s.gem' -ext_options = { - 'source_urls': [ - 'http://rubygems.org/downloads/', # gem archive - ], - 'source_tmpl': name_tmpl, -} -exts_list = [ - ('ffi', '1.9.6', ext_options), - ('childprocess', '0.5.5', ext_options), - ('json', '1.8.2', ext_options), - ('cabin', '0.7.1', ext_options), - ('backports', '3.6.4', ext_options), - ('arr-pm', '0.0.9', ext_options), - ('clamp', '0.6.4', ext_options), - ('fpm', '1.3.3', ext_options), -] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb index cce8d3ff7e..ec8aac5c94 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -31,3 +31,22 @@ configopts = "--disable-install-doc --enable-shared" moduleclass = 'lang' +name_tmpl = '%(name)s-%(version)s.gem' + +ext_options = { + 'source_urls': [ + 'http://rubygems.org/downloads/', # gem archive + ], + 'source_tmpl': name_tmpl, +} + +exts_list = [ + ('ffi', '1.9.6', ext_options), + ('childprocess', '0.5.5', ext_options), + ('json', '1.8.2', ext_options), + ('cabin', '0.7.1', ext_options), + ('backports', '3.6.4', ext_options), + ('arr-pm', '0.0.9', ext_options), + ('clamp', '0.6.4', ext_options), + ('fpm', '1.3.3', ext_options), +] -- GitLab From e77b57269e1d454e80a383ec30c5c6d1c2eea0c4 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 3 Apr 2015 16:15:04 +0200 Subject: [PATCH 202/992] added some pandas --- .../p/pandas/pandas-0.16.0-intel-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb new file mode 100644 index 0000000000..d8f4627e56 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = "pandas" +version = "0.16.0" + +homepage = "http://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.9" + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 42777cfcc27e91ed8e4803d24b4cdf89bd354dbc Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 3 Apr 2015 16:35:24 +0200 Subject: [PATCH 203/992] fixed filename --- ...0-intel-2015a.eb => pandas-0.16.0-intel-2015a-Python-2.7.9.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/pandas/{pandas-0.16.0-intel-2015a.eb => pandas-0.16.0-intel-2015a-Python-2.7.9.eb} (100%) diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb similarity index 100% rename from easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb rename to easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb -- GitLab From 476505091f8f333a882e611d068bebc32b5cb9f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Apr 2015 13:35:02 +0200 Subject: [PATCH 204/992] replace use of $root with %(installdir)s --- easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb index 355b27d3e6..9dcb92d748 100644 --- a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb @@ -53,7 +53,7 @@ sanity_check_paths = { } modextravars = { - 'BIOINFOCONFDIR': '$root/bios/conf', + 'BIOINFOCONFDIR': '%(installdir)s/bios/conf', } moduleclass = 'bio' -- GitLab From 1eb6cd64d29cd9510a131f39baf2c164268ed0a8 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 14:01:49 +0200 Subject: [PATCH 205/992] added new PyYAML with intel 2015a --- .../PyYAML-3.11-intel-2015a-Python-2.7.9.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..adc1d69d57 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = "PyYAML" +version = "3.11" + +homepage = "http://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.9" +py_short_ver = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libyaml', '0.1.4'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/yaml' % py_short_ver], +} + +moduleclass = 'lib' -- GitLab From 5a8f25c7dd5bc201dc7fa5e008db23b13439afac Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 14:11:14 +0200 Subject: [PATCH 206/992] added forgotten libyaml --- .../l/libyaml/libyaml-0.1.4-intel-2015a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb new file mode 100644 index 0000000000..6cc4254bea --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.4' + +homepage = 'http://pyyaml.org/wiki/LibYAML' +description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['yaml-%(version)s.tar.gz'] +source_urls = ['http://pyyaml.org/download/libyaml/'] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.so"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' -- GitLab From 4cd2ead1b1b4b9c9a19f6400cb7c9f6061835c53 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Fri, 3 Apr 2015 12:57:44 +0200 Subject: [PATCH 207/992] Support IPython 3.0. --- .../IPython-3.0.0-intel-2015a-Python-2.7.9.eb | 40 +++++++++++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb | 27 +++++++++++++ ...Q-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb | 31 ++++++++++++++ .../util-linux-2.22.2-intel-2015a.eb | 29 ++++++++++++++ 4 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..941a1d3d1c --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,40 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.0.0' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://archive.ipython.org/release/%(version)s/'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '2.7' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('pyzmq', '2.0.1', versionsuffix, '-zmq3'), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', "") + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb new file mode 100644 index 0000000000..9ac5fd9480 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://%s.googlecode.com/files/' % (name.lower())] +sources = ['%s-%s.tar.gz' % ('libpgm', version)] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000..022cf3fe3b --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,31 @@ +name = 'PyZMQ' +version = '2.2.0.1' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[0:2]) +zmqversion = '3.2.2' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb new file mode 100644 index 0000000000..7cdce40ba2 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.22.2' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +configopts = '--disable-chfn-chsh --disable-login --disable-su ' +configopts += '--disable-wall --disable-use-tty-group ' +configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From 5a631ddc9892e26f84e2e8cc753e71b1c9cedc1c Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 7 Apr 2015 14:47:53 +0200 Subject: [PATCH 208/992] WIP support for IPython. --- .../IPython-3.0.0-intel-2015a-Python-2.7.9.eb | 3 +- ...MQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb | 34 ++++++++++++++++++ ...requests-2.6.0-intel-2015a-Python-2.7.9.eb | 30 ++++++++++++++++ .../z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb | 36 +++++++++++++++++++ 4 files changed, 102 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb index 941a1d3d1c..bda10584b8 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb @@ -24,7 +24,8 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), ('pysqlite', '2.6.3', versionsuffix), - ('pyzmq', '2.0.1', versionsuffix, '-zmq3'), + ('PyZMQ', '14.5.0', '%s-zmq3' % versionsuffix), + ('requests', '2.6.0', versionsuffix) ] # override extensions sanity check, default filter that imports a Python module doesn't work here diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000..b297340fc3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.5.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[0:2]) +zmqversion = '3.2.2' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..4a577a2051 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.6.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pythonshortversion, version, pythonshortversion) ], +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb new file mode 100644 index 0000000000..537584a82a --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '3.2.2' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['ZeroMQ-%(version)s_icc.patch'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.22.2'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 1ef7de76cd6442722940f1c74fd8d37f35d7a9c9 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 15:54:48 +0200 Subject: [PATCH 209/992] Update libyaml-0.1.4-intel-2015a.eb --- easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb index 6cc4254bea..7b42e2d083 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'libyaml' -version = '0.1.4' +version = '0.1.6' homepage = 'http://pyyaml.org/wiki/LibYAML' description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" -- GitLab From 42afd7c6dd49bc848146fa0d6e60fd659bfb2ae2 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 15:54:57 +0200 Subject: [PATCH 210/992] Rename libyaml-0.1.4-intel-2015a.eb to libyaml-0.1.6-intel-2015a.eb --- ...{libyaml-0.1.4-intel-2015a.eb => libyaml-0.1.6-intel-2015a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/libyaml/{libyaml-0.1.4-intel-2015a.eb => libyaml-0.1.6-intel-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb rename to easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb -- GitLab From 1c9bf47a32741683d5c671afd202554f7a7ee7a4 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 15:55:07 +0200 Subject: [PATCH 211/992] Update PyYAML-3.11-intel-2015a-Python-2.7.9.eb --- .../p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb index adc1d69d57..bd74a7c6d1 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), - ('libyaml', '0.1.4'), + ('libyaml', '0.1.6'), ] options = {'modulename': 'yaml'} -- GitLab From b6a99c2a39116ce3fc6fd07e3b51415b85e0f0fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Apr 2015 17:31:32 +0200 Subject: [PATCH 212/992] stop relying on $MKLROOT in ROOT easyconfigs --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 2 +- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb index fb2d479661..55aab9105b 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb @@ -32,7 +32,7 @@ configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' # enable features configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' -configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index 6fd56a833c..c0e1e4e91e 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -32,7 +32,7 @@ configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' # enable features configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' -configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index 74c34689f1..cc50539ec7 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -36,7 +36,7 @@ configopts = ' --disable-xft --disable-xrootd --disable-mysql' # enable features configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' -configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' -- GitLab From 4f90d7aafa04678d9f6316d3eced8ea82c0fd1ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Apr 2015 17:36:49 +0200 Subject: [PATCH 213/992] fix indent --- easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb index 9dcb92d748..418cc4118e 100644 --- a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb @@ -53,7 +53,7 @@ sanity_check_paths = { } modextravars = { - 'BIOINFOCONFDIR': '%(installdir)s/bios/conf', + 'BIOINFOCONFDIR': '%(installdir)s/bios/conf', } moduleclass = 'bio' -- GitLab From 719a4f865622e804799f81f249797da18ab007e2 Mon Sep 17 00:00:00 2001 From: Petar Forai Date: Tue, 7 Apr 2015 22:49:27 +0200 Subject: [PATCH 214/992] Added Cray Toolchain Configs. --- .../easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 18 ++++++++++++++++++ .../easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 18 ++++++++++++++++++ .../easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 18 ++++++++++++++++++ .../easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 18 ++++++++++++++++++ .../c/CrayIntel/CrayIntel-5.1.29.eb | 18 ++++++++++++++++++ .../c/CrayIntel/CrayIntel-5.2.25.eb | 18 ++++++++++++++++++ 6 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb new file mode 100644 index 0000000000..940aef1f65 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.1.29' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb new file mode 100644 index 0000000000..286a0ba710 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.2.25' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..2494f6ad7d --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.1.29' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..8f621e3fe9 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.2.25' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb new file mode 100644 index 0000000000..be8eff9d45 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.1.29' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb new file mode 100644 index 0000000000..ed28f41efb --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.2.25' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + -- GitLab From 6b0e3808d926bb872e1b03863cc163185fa48978 Mon Sep 17 00:00:00 2001 From: Petar Forai Date: Tue, 7 Apr 2015 23:29:53 +0200 Subject: [PATCH 215/992] Addressed remarks. --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 11 ++--------- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 11 ++--------- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 11 ++--------- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 11 ++--------- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb | 11 ++--------- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb | 11 ++--------- 6 files changed, 12 insertions(+), 54 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb index 940aef1f65..f09961bd60 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayCCE' version = '5.1.29' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb index 286a0ba710..ff0774c751 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayCCE' version = '5.2.25' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index 2494f6ad7d..d2d1520bce 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayGNU' version = '5.1.29' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index 8f621e3fe9..afc8c6010c 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayGNU' version = '5.2.25' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb index be8eff9d45..6cb4679750 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayIntel' version = '5.1.29' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb index ed28f41efb..f24f574b3f 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayIntel' version = '5.2.25' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - -- GitLab From 0f709b5dccc6325285acd9624c88254d8b01ae92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 12:09:21 +0200 Subject: [PATCH 216/992] add easyconfig (and patch) for pyhull + Qhull with intel/2015a, set $CPATH correctly in existing Qhull easyconfigs --- .../c/CMake/CMake-3.2.1-GCC-4.9.2.eb | 22 ++++++++++++ .../pyhull-1.5.4-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ .../pyhull-1.5.4_use-provided-Qhull.patch | 26 ++++++++++++++ .../q/Qhull/Qhull-2012.1-ictce-7.1.2.eb | 4 +++ .../q/Qhull/Qhull-2012.1-intel-2014b.eb | 4 +++ .../q/Qhull/Qhull-2012.1-intel-2015a.eb | 31 +++++++++++++++++ 6 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..f556c35a24 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..c71d39213e --- /dev/null +++ b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = "pyhull" +version = "1.5.4" +homepage = "http://pythonhosted.org/pyhull/" +description = """Pyhull is a Python wrapper to qhull (http://www.qhull.org/) for the computation of the convex hull, + Delaunay triangulation and Voronoi diagram. It is written as a Python C extension, with both high-level and low-level + interfaces to qhull. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['pyhull-%(version)s_use-provided-Qhull.patch'] + +python = "Python" +pythonversion = "2.7.9" +py_short_ver = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('Qhull', '2012.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pv)s/site-packages/pyhull-%%(version)s-py%(pv)s-linux-x86_64.egg' % {'pv': py_short_ver}], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch new file mode 100644 index 0000000000..718405a70d --- /dev/null +++ b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch @@ -0,0 +1,26 @@ +let pyhull use provided Qhull rather than having it (re)build (parts of) Qhull itself +author: Kenneth Hoste (HPC-UGent) +--- pyhull-1.5.4/setup.py.orig 2015-04-07 21:30:35.000000000 +0200 ++++ pyhull-1.5.4/setup.py 2015-04-08 11:24:48.913427316 +0200 +@@ -7,14 +7,18 @@ + from setuptools import setup, Extension, find_packages + + src_dir = "src" +-include_dirs = glob.glob(os.path.join("src", "libqhull")) +-sources = glob.glob(os.path.join("src", "libqhull", "*.c")) ++include_dirs = [os.path.join(os.getenv('EBROOTQHULL'), 'include', 'libqhull')] ++library_dirs = [os.path.join(os.getenv('EBROOTQHULL'), 'lib')] ++sources = [] + if sys.platform.strip() == "darwin": + include_dirs += glob.glob(os.path.join("src", "fmemopen")) + sources += glob.glob(os.path.join("src", "fmemopen", "*.c")) + extension = Extension('pyhull._pyhull', + include_dirs=include_dirs, +- sources=[os.path.join(src_dir, '_pyhull.c')] + sources) ++ library_dirs=library_dirs, ++ libraries=['qhull'], ++ sources=[os.path.join(src_dir, '_pyhull.c')] + sources, ++ ) + + long_description = """ + Pyhull is a Python wrapper to Qhull (http://www.qhull.org/) for the diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index 9aa673f99d..dd5a337d1f 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -24,4 +24,8 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = { + 'CPATH': ['qhull/include'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index 35f7fe3a72..188d2a929c 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -24,4 +24,8 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = { + 'CPATH': ['qhull/include'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb new file mode 100644 index 0000000000..d32af2c654 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2012.1' + +homepage = 'http://www.qhull.org' +description = """ +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, +furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, +and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s-src.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = ['Qhull-2012.1-intel-fix.patch'] + +builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.so'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +moduleclass = 'math' -- GitLab From 7e51eec446f832f110baadcf32a1d2d1125102d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:14:47 +0200 Subject: [PATCH 217/992] SWIG is build dependency for python-meep, style fixes in Meep easyconfigs --- easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb | 2 +- ...on-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 12 +++++------- .../python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb | 12 +++++------- .../python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb | 12 +++++------- 5 files changed, 17 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb index 99b133b3f5..15da01ed14 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -patches = ['Meep-%s_version-string-without-spaces.patch' % version] +patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.3.1'), diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb index 67e5d881fb..475c5f321c 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -patches = ['Meep-%s_version-string-without-spaces.patch' % version] +patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.3.1'), diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 2643e2c09c..082e6cbbfd 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -10,18 +10,16 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] sources = [SOURCELOWER_TAR] -patches = [ - 'MPI_destructor_1.3.patch' - ] +patches = ['MPI_destructor_1.3.patch'] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('Meep', '1.2'), - ('SWIG', '2.0.4', '-%s-%s' % (python, pythonver)) - ] + (python, pythonver), + ('Meep', '1.2'), +] +builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb index 67aaeea480..8656294b31 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb @@ -10,18 +10,16 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] sources = [SOURCELOWER_TAR] -patches = [ - 'MPI_destructor_1.3.patch' - ] +patches = ['MPI_destructor_1.3.patch'] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('Meep', '1.2'), - ('SWIG', '2.0.4', '-%s-%s' % (python, pythonver)) - ] + (python, pythonver), + ('Meep', '1.2'), +] +builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb index dccd4207fd..82f6fac9ed 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb @@ -10,18 +10,16 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] sources = [SOURCELOWER_TAR] -patches = [ - 'MPI_destructor_1.3.patch' - ] +patches = ['MPI_destructor_1.3.patch'] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('Meep', '1.2'), - ('SWIG', '2.0.4', '-%s-%s' % (python, pythonver)) - ] + (python, pythonver), + ('Meep', '1.2'), +] +builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' -- GitLab From 624f2876e96c7e4f6f38e78fec5f0d6a25a4f697 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:16:10 +0200 Subject: [PATCH 218/992] add easyconfig for python-meep 1.4.2 on top of Python/2.7.9 and Meep/1.3 --- .../g/GMP/GMP-5.0.5-intel-2015a.eb | 22 ++++++++++++ .../g/guile/guile-1.8.8-intel-2015a.eb | 31 ++++++++++++++++ .../h/Harminv/Harminv-1.4-intel-2015a.eb | 19 ++++++++++ .../l/libctl/libctl-3.2.2-intel-2015a.eb | 20 +++++++++++ .../l/libffi/libffi-3.0.13-intel-2015a.eb | 25 +++++++++++++ .../l/libtool/libtool-2.4.2-intel-2015a.eb | 15 ++++++++ .../libunistring-0.9.3-intel-2015a.eb | 26 ++++++++++++++ .../m/Meep/Meep-1.3-intel-2015a.eb | 35 +++++++++++++++++++ .../pkg-config-0.27.1-intel-2015a.eb | 27 ++++++++++++++ ...1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb | 27 ++++++++++++++ .../SWIG-3.0.5-intel-2015a-Python-2.7.9.eb | 23 ++++++++++++ 11 files changed, 270 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.0.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-intel-2015a.eb new file mode 100644 index 0000000000..21b43d921f --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '5.0.5' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, + operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb new file mode 100644 index 0000000000..abc19c54da --- /dev/null +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.2'), + ('GMP', '5.0.5'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.27.1'), + ('libffi', '3.0.13'), + ('libreadline', '6.2'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb new file mode 100644 index 0000000000..8b0afc7b1f --- /dev/null +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'Harminv' +version = '1.4' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given + a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) + in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} + +source_urls = ['http://ab-initio.mit.edu/harminv/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --with-blas=mkl_em64t --with-lapack=mkl_em64t --enable-shared" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb new file mode 100644 index 0000000000..0de2f0bd93 --- /dev/null +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libctl' +version = '3.2.2' + +homepage = 'http://ab-initio.mit.edu/libctl' +description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +source_urls = ['http://ab-initio.mit.edu/libctl/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('guile', '1.8.8')] + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb new file mode 100644 index 0000000000..1a559500ae --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.0.13' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['libffi-%(version)s_include-xmmintrin.patch'] + +sanity_check_paths = { + 'files': ['lib/libffi.%s' % SHLIB_EXT, 'lib/libffi.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb new file mode 100644 index 0000000000..eddb4ada02 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.2' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb new file mode 100644 index 0000000000..93d202fc27 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['libunistring_icc_builtin_nan-inf.patch'] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.so', 'include/unistring'] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb new file mode 100644 index 0000000000..270e349f06 --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Meep' +version = '1.3' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/Meep' +description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package + developed at MIT to model electromagnetic systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [ + 'http://ab-initio.mit.edu/meep/', + 'http://ab-initio.mit.edu/meep/old/', +] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['Meep-1.2_version-string-without-spaces.patch'] + +dependencies = [ + ('Harminv', '1.4'), + ('HDF5', '1.8.14', '-gpfs'), + ('libctl', '3.2.2'), + ('GSL', '1.16'), + ('FFTW', '3.3.4') +] + +configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " +configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb new file mode 100644 index 0000000000..ddfabeac31 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.27.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb new file mode 100644 index 0000000000..0da5220c97 --- /dev/null +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb @@ -0,0 +1,27 @@ +name = 'python-meep' +version = '1.4.2' + +homepage = 'https://code.launchpad.net/python-meep' +description = """Python wrapper for the Meep FDTD solver.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} + +source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] +sources = [SOURCELOWER_TAR] + +patches = ['MPI_destructor_1.3.patch'] + +python = 'Python' +pythonver = '2.7.9' +meep = 'Meep' +meepver = '1.3' +versionsuffix = '-%s-%s-%s-%s' % (python, pythonver, meep, meepver) + +dependencies = [ + (python, pythonver), + (meep, meepver), +] +builddependencies = [('SWIG', '3.0.5', '-%s-%s' % (python, pythonver))] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..3193585375 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '3.0.5' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.36'), +] + +moduleclass = 'devel' -- GitLab From 42a68f8a93daf6e82791432ccb857a55cf7a41bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:25:17 +0200 Subject: [PATCH 219/992] fix patch for Meep v1.3 --- easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb | 2 +- .../Meep/Meep-1.3_version-string-without-spaces.patch | 11 +++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb index 270e349f06..822615186c 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -patches = ['Meep-1.2_version-string-without-spaces.patch'] +patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.4'), diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch b/easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch new file mode 100644 index 0000000000..90cebc9859 --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch @@ -0,0 +1,11 @@ +--- meep-1.3/libctl/Makefile.in.orig 2015-03-31 17:47:53.000000000 +0200 ++++ meep-1.3/libctl/Makefile.in 2015-04-08 13:23:54.206192661 +0200 +@@ -369,7 +369,7 @@ + ############################################################################## + + # what is printed out when invoking your program with --version: +-VERSION_STRING = "Meep @VERSION@, Copyright (C) 2005-2015 Massachusetts Insitute of Technology." ++VERSION_STRING = "Meep_@VERSION@,_Copyright_(C)_2005-2015_Massachusetts_Insitute_of_Technology." + MY_DEFS = -DHAVE_CTL_HOOKS=1 -DHAVE_CTL_EXPORT_HOOK=1 + PROGRAM_NAME = meep + SPECIFICATION_FILE = $(PROGRAM_NAME).scm -- GitLab From 6c00f9fb66c618ea421c6b1e7c68dad7ea2a2543 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:48:32 +0200 Subject: [PATCH 220/992] stick to SWIG 2.x for pyhton-meep --- ...1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb | 2 +- .../SWIG-2.0.12-intel-2015a-Python-2.7.9.eb | 23 +++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb index 0da5220c97..f9f82b9d18 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb @@ -22,6 +22,6 @@ dependencies = [ (python, pythonver), (meep, meepver), ] -builddependencies = [('SWIG', '3.0.5', '-%s-%s' % (python, pythonver))] +builddependencies = [('SWIG', '2.0.12', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f049ac6af0 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '2.0.12' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.36'), +] + +moduleclass = 'devel' -- GitLab From f0c8dcfae8501554cfd63862bfa0b441efae38e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:53:07 +0200 Subject: [PATCH 221/992] add pandas extension to Python 2.7.9 easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 0f382d98ba..d228f95a16 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -107,6 +107,9 @@ exts_list = [ ('pytz', '2014.10', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 4ec2b0ce97..e667c4f618 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -107,6 +107,9 @@ exts_list = [ ('pytz', '2014.10', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index db9c0d75b8..06dcabeb70 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -110,6 +110,9 @@ exts_list = [ ('pytz', '2014.10', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' -- GitLab From 359a12c02b15b329634fd515b3141e29a5e7fdd9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 14:17:17 +0200 Subject: [PATCH 222/992] fix remark, bump libreadline in guile easyconfig to 6.3 --- easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb | 2 +- .../python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 1 + .../python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb | 1 + .../p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb | 1 + .../python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb | 1 + 5 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb index abc19c54da..d66e7cf118 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('libunistring', '0.9.3'), ('pkg-config', '0.27.1'), ('libffi', '3.0.13'), - ('libreadline', '6.2'), + ('libreadline', '6.3'), ] configopts = " --enable-error-on-warning=no" diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 082e6cbbfd..ee4f9a4c40 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -20,6 +20,7 @@ dependencies = [ (python, pythonver), ('Meep', '1.2'), ] + builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb index 8656294b31..562323eb53 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb @@ -20,6 +20,7 @@ dependencies = [ (python, pythonver), ('Meep', '1.2'), ] + builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb index 82f6fac9ed..afe2d60a9b 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb @@ -20,6 +20,7 @@ dependencies = [ (python, pythonver), ('Meep', '1.2'), ] + builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb index f9f82b9d18..bfb66e3979 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb @@ -22,6 +22,7 @@ dependencies = [ (python, pythonver), (meep, meepver), ] + builddependencies = [('SWIG', '2.0.12', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' -- GitLab From 1ec86e9797f2c27805ca03034fd796d2dd6e7709 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:06:27 +0200 Subject: [PATCH 223/992] Added LAPACK-3.5.0-gompi-1.5.16.eb --- LAPACK-3.5.0-gompi-1.5.16.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 LAPACK-3.5.0-gompi-1.5.16.eb diff --git a/LAPACK-3.5.0-gompi-1.5.16.eb b/LAPACK-3.5.0-gompi-1.5.16.eb new file mode 100644 index 0000000000..0027dce752 --- /dev/null +++ b/LAPACK-3.5.0-gompi-1.5.16.eb @@ -0,0 +1,15 @@ +name = 'LAPACK' +version = "3.5.0" + +homepage = 'http://www.netlib.org/lapack/' +description = """LAPACK is written in Fortran90 and provides routines for solving systems of + simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue + problems, and singular value problems.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = [homepage] + +moduleclass = 'numlib' -- GitLab From 3b3cab12c5ae47fb540c24c3f9069006db5702a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:06:57 +0200 Subject: [PATCH 224/992] Added OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0 --- OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 52 ++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb diff --git a/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..fe4211f53c --- /dev/null +++ b/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.13' + +lapackver = '3.5.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' -- GitLab From 917b1507a2042f4b0cb8dd0b26fbb5ee77668169 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:07:36 +0200 Subject: [PATCH 225/992] Added FFTW-3.3.4-gompi-1.5.16 --- FFTW-3.3.4-gompi-1.5.16.eb | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 FFTW-3.3.4-gompi-1.5.16.eb diff --git a/FFTW-3.3.4-gompi-1.5.16.eb b/FFTW-3.3.4-gompi-1.5.16.eb new file mode 100644 index 0000000000..6ae444ae02 --- /dev/null +++ b/FFTW-3.3.4-gompi-1.5.16.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 265f11d2a8c4be3d91b7821b2bac123aeb82fa8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:08:19 +0200 Subject: [PATCH 226/992] Added ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0 --- ...mpi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb diff --git a/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..a52473e7ff --- /dev/null +++ b/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff)] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 6bcfeee22cce3af60a529eaa801a54c5944e8eb2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:08:52 +0200 Subject: [PATCH 227/992] Added goolf-1.5.16 --- goolf-1.5.16.eb | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 goolf-1.5.16.eb diff --git a/goolf-1.5.16.eb b/goolf-1.5.16.eb new file mode 100644 index 0000000000..e9cea8d51b --- /dev/null +++ b/goolf-1.5.16.eb @@ -0,0 +1,37 @@ +easyblock = "Toolchain" + +name = 'goolf' +version = '1.5.16' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_version = '4.8.3' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blas = '%s-%s' % (blaslib, blasver) +blas_suff = '-LAPACK-3.5.0' + +# toolchain used to build goolf dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, + ('OpenMPI', '1.6.5', '', comp), # part of gompi-1.5.16 + (blaslib, blasver, blas_suff, comp_mpi_tc), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blas_suff), comp_mpi_tc) +] + +moduleclass = 'toolchain' -- GitLab From 589908c611d3899c8e3e9fbaa02105ff50281c8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:21:42 +0200 Subject: [PATCH 228/992] easyconfigs moved to the right directories --- .../easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb | 0 .../easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb | 0 .../o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 0 .../ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename FFTW-3.3.4-gompi-1.5.16.eb => easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb (100%) rename LAPACK-3.5.0-gompi-1.5.16.eb => easybuild/easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb (100%) rename OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb => easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb (100%) rename ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb => easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb (100%) diff --git a/FFTW-3.3.4-gompi-1.5.16.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb similarity index 100% rename from FFTW-3.3.4-gompi-1.5.16.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb diff --git a/LAPACK-3.5.0-gompi-1.5.16.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb similarity index 100% rename from LAPACK-3.5.0-gompi-1.5.16.eb rename to easybuild/easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb diff --git a/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb similarity index 100% rename from OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb diff --git a/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb similarity index 100% rename from ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb -- GitLab From 026f640280842616cbb3aa9a2461b9c66444827e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:48:35 +0200 Subject: [PATCH 229/992] goolf-1.5.16 moved to the right directory --- goolf-1.5.16.eb => easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename goolf-1.5.16.eb => easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb (100%) diff --git a/goolf-1.5.16.eb b/easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb similarity index 100% rename from goolf-1.5.16.eb rename to easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb -- GitLab From 597d8d8d4f62739c956f9b8cd431aeb96ff7525c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 16:21:52 +0200 Subject: [PATCH 230/992] Added HPL-2.0-goolf-1.5.16.eb --- .../easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb new file mode 100644 index 0000000000..d327bfbbab --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.0' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic +on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the +High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 68012ca4f308fa11d9bff36163d41ad913384c5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 21:18:34 +0200 Subject: [PATCH 231/992] {data}[intel/2015a] h5py 2.5.0 (REVIEW) --- ...5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb new file mode 100644 index 0000000000..108b726ecc --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': False} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +hdf5suff = '-gpfs' +versionsuffix = '-%s-%s%s' % (python, pythonver, hdf5suff) + +dependencies = [ + (python, pythonver), + ('HDF5', '1.8.14', hdf5suff), +] + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 5a881154a9d5bfd525dc3ae6a15f3ecb0ec95fc5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 21:20:51 +0200 Subject: [PATCH 232/992] {math}[intel/2015a] numpy 1.9.2 + scipy 0.15.1 (REVIEW) --- .../numpy-1.9.2-intel-2015a-Python-2.7.9.eb | 26 +++++++++++++++++++ .../scipy-0.15.1-intel-2015a-Python-2.7.9.eb | 19 ++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..bc4a69d14c --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f67514e591 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' -- GitLab From ee6196e68bae9e32808d708233440c569ad74500 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 21:48:51 +0200 Subject: [PATCH 233/992] {vis}[intel/2015a] grace 5.1.23 (REVIEW) --- .../g/grace/grace-5.1.23-intel-2015a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb new file mode 100644 index 0000000000..208d216f7b --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.23' + +homepage = 'http://freecode.com/projects/grace' +description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2015a'} + +dependencies = [ + ('motif', '2.3.4', '-libX11-1.6.3'), + ('netCDF', '4.3.2'), +] + +runtest = 'tests' + +# we also need to run make links right before or after make install. +installopts = 'links' + +sanity_check_paths = { + 'files': ['bin/xmgrace'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From e37e42a351a2dcfc55e6b7a82768600fe1acf6a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 10:19:41 +0200 Subject: [PATCH 234/992] add easyconfigs for WIEN2k 14.1 and 14.2 with intel/2015a --- .../w/WIEN2k/WIEN2k-14.1-intel-2015a.eb | 46 +++++++++++++++++++ .../w/WIEN2k/WIEN2k-14.2-intel-2015a.eb | 40 ++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb new file mode 100644 index 0000000000..a5d641a90f --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb @@ -0,0 +1,46 @@ +name = 'WIEN2k' +version = '14.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['b926596ea86d505120af8829cec4814e'] + +patches = [ + 'WIEN2k-%(version)s_lapw5-main-accuracy-fix.patch', + 'WIEN2k-%(version)s_fix-tetra.patch', + 'WIEN2k-%(version)s_fix-x_lapw.patch', +] + +dependencies = [('FFTW', '3.3.4')] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb new file mode 100644 index 0000000000..5149928839 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb @@ -0,0 +1,40 @@ +name = 'WIEN2k' +version = '14.2' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['1179be3b3bcb021af4c65fefea579ca6'] + +dependencies = [('FFTW', '3.3.4')] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), +] + +moduleclass = 'chem' -- GitLab From 838b269bf30cdb61ccdc69e7a6ef3deed8995455 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Thu, 9 Apr 2015 12:59:00 +0200 Subject: [PATCH 235/992] Added GDAL-1.9.2-goolf-1.5.16 and zlib-1.2.8 dependency --- .../g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb | 24 +++++++++++++++++++ .../z/zlib/zlib-1.2.8-goolf-1.5.16.eb | 22 +++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb new file mode 100644 index 0000000000..14deb76474 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '1.9.2' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ['http://download.osgeo.org/gdal/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ['lib/libgdal.so', 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb new file mode 100644 index 0000000000..9b56c2bffb --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From c72cd834e99c897e89f4b93d4f1a9bd1b1155004 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 13:36:29 +0200 Subject: [PATCH 236/992] fix remar --- .../h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb index 108b726ecc..d6f4de7c55 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb @@ -9,24 +9,24 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to amounts of data.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'usempi': False} +toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[0:2]) hdf5suff = '-gpfs' -versionsuffix = '-%s-%s%s' % (python, pythonver, hdf5suff) +versionsuffix = '-%s-%s%s' % (python, pyver, hdf5suff) dependencies = [ - (python, pythonver), + (python, pyver), ('HDF5', '1.8.14', hdf5suff), ] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], + 'files': ['lib/python%(pv)s/site-packages/%%(name)s-%%(version)s-py%(pv)s-linux-x86_64.egg' % {'pv': pyshortver}], 'dirs': [], } -- GitLab From b5a1b36a088fed3e74c8594b5b8cbaae72fcaaff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 13:56:43 +0200 Subject: [PATCH 237/992] add easyconfigs for monty 0.6.4 and latest dev version by @gmatteo --- ...tel-2015a-Python-2.7.9-gmatteo-20150325.eb | 36 +++++++++++++++++++ .../monty-0.6.4-intel-2015a-Python-2.7.9.eb | 35 ++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb create mode 100644 easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb new file mode 100644 index 0000000000..14e4a5ef3b --- /dev/null +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'monty' +version = '0.6.4' + +homepage = 'http://pypi.python.org/pypi/monty/' +description = """Monty implements supplementary useful functions for Python that are not part of the standard library. + Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton + and cached_class, and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/gmatteo/monty/archive/'] +sources = ['3152d41.tar.gz'] +checksums = ['d8afe0556fd29191e66babb31750b7c4'] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s-gmatteo-20150325' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PyYAML', '3.11', '-%s-%s' % (python, pythonversion)), +] + +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..7d2b055f0b --- /dev/null +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'monty' +version = '0.6.4' + +homepage = 'http://pypi.python.org/pypi/monty/' +description = """Monty implements supplementary useful functions for Python that are not part of the standard library. + Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton + and cached_class, and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PyYAML', '3.11', versionsuffix), +] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 81a2023fabbd4db4e95b6da25b663b08501efc0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 14:46:38 +0200 Subject: [PATCH 238/992] fix remark --- ...ty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb index 14e4a5ef3b..1dfd105d74 100644 --- a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb @@ -10,14 +10,17 @@ description = """Monty implements supplementary useful functions for Python that toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://github.com/gmatteo/monty/archive/'] -sources = ['3152d41.tar.gz'] +commit = '3152d41' +extrasuff = 'gmatteo-20150325' + +source_urls = ['https://github.com/gmatteo/monty/archive/%s.tar.gz#' % commit] +sources = ['%%(name)s-%%(version)s-%s.tar.gz' % extrasuff] checksums = ['d8afe0556fd29191e66babb31750b7c4'] python = 'Python' pythonversion = '2.7.9' -versionsuffix = '-%s-%s-gmatteo-20150325' % (python, pythonversion) +versionsuffix = '-%s-%s-%s' % (python, pythonversion, extrasuff) dependencies = [ (python, pythonversion), -- GitLab From 9f2d54c31bf5d52e27f5da2c064c5f0bb503788c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 14:51:44 +0200 Subject: [PATCH 239/992] {chem}[intel/2015a] pymatgen 3.0.13 + spglib 1.7.3 (REVIEW) --- ...tel-2015a-Python-2.7.9-gmatteo-20150407.eb | 39 +++++++++++++++++++ ...ymatgen-3.0.13-intel-2015a-Python-2.7.9.eb | 35 +++++++++++++++++ .../s/spglib/spglib-1.7.3-intel-2015a.eb | 21 ++++++++++ 3 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb new file mode 100644 index 0000000000..8e35e9a845 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb @@ -0,0 +1,39 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '3.0.13' + +homepage = 'http://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +commit = 'd9b9a17' +extrasuff = 'gmatteo-20150407' + +source_urls = ['https://github.com/gmatteo/pymatgen/archive/%s.tar.gz#' % commit] +sources = ['%%(name)s-%%(version)s-%s.tar.gz' % extrasuff] +checksums = ['461ad0f8bb8109f547dc3b708240f85f'] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, extrasuff) + +dependencies = [ + (python, pythonversion), + ('spglib', '1.7.3'), +] + +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': ['bin/pmg', 'bin/ipmg', + ("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..73ac37040a --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '3.0.13' + +homepage = 'http://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('spglib', '1.7.3'), +] + +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': ['bin/pmg', 'bin/ipmg', + ("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb new file mode 100644 index 0000000000..f6b34ab670 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.so'], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' -- GitLab From ac4f675693433096562844f8cb97cd3a2f9d33b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 16:23:44 +0200 Subject: [PATCH 240/992] {bio}[intel/2015a] FSL 5.0.8 + deps (REVIEW) --- .../f/FSL/FSL-5.0.8-intel-2015a.eb | 24 +++++++++++++++++ .../fixesproto/fixesproto-5.0-intel-2015a.eb | 19 ++++++++++++++ .../f/freeglut/freeglut-2.8.1-intel-2015a.eb | 21 +++++++++++++++ .../inputproto/inputproto-2.3-intel-2015a.eb | 19 ++++++++++++++ .../libXfixes/libXfixes-5.0.1-intel-2015a.eb | 24 +++++++++++++++++ .../l/libXi/libXi-1.7.4-intel-2015a.eb | 26 +++++++++++++++++++ 6 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb new file mode 100644 index 0000000000..dd4d60386c --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'FSL' +version = '5.0.8' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-%(version)s_ictce-wd803.patch', + 'FSL_icc_nan-inf_fix.patch', +] + +dependencies = [ + ('freeglut', '2.8.1'), + ('expat', '2.1.0'), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb new file mode 100644 index 0000000000..5d430a5301 --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb new file mode 100644 index 0000000000..f501cd2fef --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'freeglut' +version = '2.8.1' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +dependencies = [('libXi', '1.7.4')] + +sanity_check_paths = { + 'files': ['lib/libglut.a', 'lib/libglut.so'], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb new file mode 100644 index 0000000000..0437a042db --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb new file mode 100644 index 0000000000..3129ec62b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.so'], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb new file mode 100644 index 0000000000..20988d4e6e --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('xproto', '7.0.27'), + ('xextproto', '7.3.0'), + ('libXext', '1.3.3'), + ('inputproto', '2.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.so', 'lib/libXi.a'], + 'dirs' : [], +} + +moduleclass = 'vis' -- GitLab From a18dadcaa3b0401c4c7fdf1d826147da8957a989 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 16:37:44 +0200 Subject: [PATCH 241/992] add missing patch file for FSL --- .../f/FSL/FSL-5.0.8_makefile_fixes.patch | 343 ++++++++++++++++++ 1 file changed, 343 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch new file mode 100644 index 0000000000..908f2f4205 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch @@ -0,0 +1,343 @@ +diff -ru fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-darwin10-gcc4.2/systemvars.mk +--- fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk 2009-11-03 18:02:14.000000000 +0100 ++++ fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2013-05-14 22:43:15.344366000 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-darwin7-gcc3.1/systemvars.mk +--- fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2013-05-14 22:43:15.363590000 +0200 +@@ -7,8 +7,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-darwin7-gcc3.3/systemvars.mk +--- fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2013-05-14 22:43:15.385466000 +0200 +@@ -7,8 +7,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-darwin8-gcc4.0/systemvars.mk +--- fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk 2007-12-19 15:40:57.000000000 +0100 ++++ fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2013-05-14 22:43:15.402328000 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-darwin9-gcc4.0/systemvars.mk +--- fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk 2007-12-19 15:33:53.000000000 +0100 ++++ fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2013-05-14 22:43:15.415331000 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk +--- fsl.orig/config/generic/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/generic/systemvars.mk 2013-05-14 22:43:15.438919000 +0200 +@@ -16,8 +16,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2013-05-14 22:43:15.455595000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc-2 +-CXX = c++-2 ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2013-05-14 22:43:15.473639000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2013-05-14 22:43:15.494398000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2.96/systemvars.mk +--- fsl.orig/config/linux_32-gcc2.96/systemvars.mk 2007-07-25 17:21:07.000000000 +0200 ++++ fsl/config/linux_32-gcc2.96/systemvars.mk 2013-05-14 22:43:15.507210000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3.2/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.2/systemvars.mk 2007-07-25 17:21:08.000000000 +0200 ++++ fsl/config/linux_32-gcc3.2/systemvars.mk 2013-05-14 22:43:15.524309000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3.3/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.3/systemvars.mk 2007-07-25 17:21:09.000000000 +0200 ++++ fsl/config/linux_32-gcc3.3/systemvars.mk 2013-05-14 22:43:15.539643000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3.4/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.4/systemvars.mk 2007-07-25 17:21:10.000000000 +0200 ++++ fsl/config/linux_32-gcc3.4/systemvars.mk 2013-05-14 22:43:15.559881000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4.0/systemvars.mk +--- fsl.orig/config/linux_32-gcc4.0/systemvars.mk 2007-07-25 17:21:11.000000000 +0200 ++++ fsl/config/linux_32-gcc4.0/systemvars.mk 2013-05-14 22:43:15.573696000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4.1/systemvars.mk +--- fsl.orig/config/linux_32-gcc4.1/systemvars.mk 2012-04-20 11:37:28.000000000 +0200 ++++ fsl/config/linux_32-gcc4.1/systemvars.mk 2013-05-14 22:43:15.590022000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3.4/systemvars.mk +--- fsl.orig/config/linux_64-gcc3.4/systemvars.mk 2007-07-25 17:21:12.000000000 +0200 ++++ fsl/config/linux_64-gcc3.4/systemvars.mk 2013-05-14 22:43:15.605655000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4.0/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.0/systemvars.mk 2007-07-25 17:21:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.0/systemvars.mk 2013-05-14 22:43:15.624046000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4.1/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.1/systemvars.mk 2007-07-25 11:19:45.000000000 +0200 ++++ fsl/config/linux_64-gcc4.1/systemvars.mk 2013-05-14 22:43:15.635678000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4.2/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.2/systemvars.mk 2008-06-26 15:25:42.000000000 +0200 ++++ fsl/config/linux_64-gcc4.2/systemvars.mk 2013-05-14 22:43:15.648658000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4.4/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.4/systemvars.mk 2012-08-22 17:17:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.4/systemvars.mk 2014-06-14 23:23:58.456480000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk +--- fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 ++++ fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2013-05-14 22:43:15.658171000 +0200 +@@ -5,8 +5,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + + ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer + +diff -ru fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk +--- fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 ++++ fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2013-05-14 22:43:15.674176000 +0200 +@@ -5,8 +5,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + + ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer + ARCHLDFLAGS = -static +diff -ru fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile +--- fsl.orig/src/libmeshutils/Makefile 2012-07-23 15:25:20.000000000 +0200 ++++ fsl/src/libmeshutils/Makefile 2013-05-14 22:43:15.320209000 +0200 +@@ -3,7 +3,7 @@ + + PROJNAME = meshUtils + +-LD_LIBRARY_PATH=${FSLDIR}/lib ++#LD_LIBRARY_PATH=${FSLDIR}/lib + + USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} + USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} +diff -ru fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile +--- fsl.orig/src/melodic/Makefile 2013-03-13 21:22:35.000000000 +0100 ++++ fsl/src/melodic/Makefile 2013-05-14 22:44:13.016352000 +0200 +@@ -3,7 +3,7 @@ + include ${FSLCONFDIR}/default.mk + + OPTFLAGS = -O3 -Wno-deprecated -ggdb +-OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui ++#OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui + + PROJNAME = melodic + +--- fsl/src/film/Makefile.orig 2014-06-15 00:43:34.908901000 +0200 ++++ fsl/src/film/Makefile 2014-06-15 00:43:52.303973000 +0200 +@@ -26,7 +26,7 @@ + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} + + film_gls:${OBJS} film_gls.o +- ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -l giftiio ++ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -lgiftiio + + film_gls_res:${OBJS} film_gls_res.o + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls_res.o ${LIBS} -- GitLab From 70f461af0c36d24eeedc3cdb28215d186b26cd23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 16:56:32 +0200 Subject: [PATCH 242/992] {chem}[intel/2015a] ABINIT 7.11.6 + libxc 2.2.2 (WIP) --- .../a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 29 +++++++++++++++++ .../l/libxc/libxc-2.2.2-intel-2015a.eb | 32 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb new file mode 100644 index 0000000000..e5ab48448f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.11.6' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c8b166ec8e65ad1d795d42b889fd772b'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-netcdf-libs="-L$EBROOTLIBXC/lib -lxc" ' +configopts += "fcflags_opt_43_ptgroups='-O0 -g -extend-source'" + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb new file mode 100644 index 0000000000..25c12f798e --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From 7855d8bc89e23f990ab0a32703cd16d209067fb2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 17:11:42 +0200 Subject: [PATCH 243/992] add another missing patch file for FSL --- .../f/FSL/FSL-5.0.8_ictce-wd803.patch | 300 ++++++++++++++++++ 1 file changed, 300 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch new file mode 100644 index 0000000000..c798885107 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch @@ -0,0 +1,300 @@ +diff -ru fsl.orig/fsl/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-darwin10-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2013-05-15 00:14:37.710187000 +0200 ++++ fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2013-05-15 00:19:46.085324000 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin11-gcc4.2/systemvars.mk fsl/config/apple-darwin11-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin11-gcc4.2/systemvars.mk 2012-03-21 12:30:53.000000000 +0100 ++++ fsl/config/apple-darwin11-gcc4.2/systemvars.mk 2013-05-15 00:19:48.066557000 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 ++OPTFLAGS := -O3 -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + ANSI_FLAGS = ${GNU_ANSI_FLAGS} +diff -ru fsl.orig/fsl/config/apple-darwin12-gcc4.2/systemvars.mk fsl/config/apple-darwin12-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin12-gcc4.2/systemvars.mk 2013-04-09 18:00:32.000000000 +0200 ++++ fsl/config/apple-darwin12-gcc4.2/systemvars.mk 2013-05-15 00:19:49.812861000 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 ++OPTFLAGS := -O3 -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + ANSI_FLAGS = ${GNU_ANSI_FLAGS} +diff -ru fsl.orig/fsl/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-darwin7-gcc3.1/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2013-05-15 00:14:37.712623000 +0200 ++++ fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2013-05-15 00:19:51.866756000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -traditional-cpp -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-darwin7-gcc3.3/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2013-05-15 00:14:37.737794000 +0200 ++++ fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2013-05-15 00:19:53.537845000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-darwin8-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2013-05-15 00:14:37.745810000 +0200 ++++ fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2013-05-15 00:19:55.229757000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-darwin9-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2013-05-15 00:14:37.751696000 +0200 ++++ fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2013-05-15 00:19:57.417620000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/generic/systemvars.mk fsl/config/generic/systemvars.mk +--- fsl.orig/fsl/config/generic/systemvars.mk 2013-05-15 00:14:37.757155000 +0200 ++++ fsl/config/generic/systemvars.mk 2013-05-15 00:19:59.724851000 +0200 +@@ -25,7 +25,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/gnu_64-gcc4.4/systemvars.mk fsl/config/gnu_64-gcc4.4/systemvars.mk +--- fsl.orig/fsl/config/gnu_64-gcc4.4/systemvars.mk 2011-04-19 10:47:52.000000000 +0200 ++++ fsl/config/gnu_64-gcc4.4/systemvars.mk 2013-05-15 00:20:03.204842000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk +--- fsl.orig/fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2013-05-15 00:14:37.763457000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2013-05-15 00:20:05.347565000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk +--- fsl.orig/fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2013-05-15 00:14:37.769108000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2013-05-15 00:20:06.913095000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk +--- fsl.orig/fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2013-05-15 00:14:37.775138000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2013-05-15 00:20:08.480567000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2.96/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc2.96/systemvars.mk 2013-05-15 00:14:37.781755000 +0200 ++++ fsl/config/linux_32-gcc2.96/systemvars.mk 2013-05-15 00:20:10.043882000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3.2/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc3.2/systemvars.mk 2013-05-15 00:14:37.787130000 +0200 ++++ fsl/config/linux_32-gcc3.2/systemvars.mk 2013-05-15 00:20:11.484066000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3.3/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc3.3/systemvars.mk 2013-05-15 00:14:37.794387000 +0200 ++++ fsl/config/linux_32-gcc3.3/systemvars.mk 2013-05-15 00:20:12.921148000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3.4/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc3.4/systemvars.mk 2013-05-15 00:14:37.799247000 +0200 ++++ fsl/config/linux_32-gcc3.4/systemvars.mk 2013-05-15 00:20:14.478184000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc4.0/systemvars.mk 2013-05-15 00:14:37.805358000 +0200 ++++ fsl/config/linux_32-gcc4.0/systemvars.mk 2013-05-15 00:20:16.819361000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4.1/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc4.1/systemvars.mk 2013-05-15 00:14:37.811876000 +0200 ++++ fsl/config/linux_32-gcc4.1/systemvars.mk 2013-05-15 00:20:18.322853000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3.4/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc3.4/systemvars.mk 2013-05-15 00:14:37.817395000 +0200 ++++ fsl/config/linux_64-gcc3.4/systemvars.mk 2013-05-15 00:20:20.465845000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.0/systemvars.mk 2013-05-15 00:14:37.823453000 +0200 ++++ fsl/config/linux_64-gcc4.0/systemvars.mk 2013-05-15 00:20:22.065237000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4.1/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.1/systemvars.mk 2013-05-15 00:14:37.829561000 +0200 ++++ fsl/config/linux_64-gcc4.1/systemvars.mk 2013-05-15 00:20:23.601865000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.2/systemvars.mk 2013-05-15 00:14:37.835868000 +0200 ++++ fsl/config/linux_64-gcc4.2/systemvars.mk 2013-05-15 00:20:25.058756000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4.4/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.4/systemvars.mk 2012-08-22 17:17:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.4/systemvars.mk 2013-05-15 00:20:26.561348000 +0200 +@@ -29,7 +29,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk +--- fsl.orig/fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2013-05-15 00:14:37.841452000 +0200 ++++ fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2013-05-15 00:20:28.072793000 +0200 +@@ -12,7 +12,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk +--- fsl.orig/fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2013-05-15 00:14:37.847832000 +0200 ++++ fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2013-05-15 00:20:29.505593000 +0200 +@@ -12,7 +12,7 @@ + ARCHLDFLAGS = -static + DEPENDFLAGS = -MM + +-OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn -- GitLab From 9fd5c72eb012bb71f7307a2472ab0d7edcfe7206 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 13 Apr 2015 09:36:10 +0200 Subject: [PATCH 244/992] First try at GCC 5.1 --- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 47 + .../GCC/mpfr-3.1.2-allpatches-20141204.patch | 1628 +++++++++++++++++ 2 files changed, 1675 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb new file mode 100644 index 0000000000..7a65f31c78 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -0,0 +1,47 @@ +name = "GCC" +version = '5.1.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '37cdc2eb0adf92e421c0841748ac1471', # gcc-5.1.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +#withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch b/easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch new file mode 100644 index 0000000000..df1aaea434 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch @@ -0,0 +1,1628 @@ +# All mpfr patches as of 2014-12-04 +# taken from their website: http://www.mpfr.org/mpfr-current/#download +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-09-26 10:52:52.000000000 +0000 +@@ -0,0 +1 @@ ++exp_2 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-03-13 15:37:28.000000000 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-09-26 10:52:52.000000000 +0000 +@@ -1 +1 @@ +-3.1.2 ++3.1.2-p1 +diff -Naurd mpfr-3.1.2-a/src/exp_2.c mpfr-3.1.2-b/src/exp_2.c +--- mpfr-3.1.2-a/src/exp_2.c 2013-03-13 15:37:28.000000000 +0000 ++++ mpfr-3.1.2-b/src/exp_2.c 2013-09-26 10:52:52.000000000 +0000 +@@ -204,7 +204,7 @@ + for (k = 0; k < K; k++) + { + mpz_mul (ss, ss, ss); +- exps <<= 1; ++ exps *= 2; + exps += mpz_normalize (ss, ss, q); + } + mpfr_set_z (s, ss, MPFR_RNDN); +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-03-13 15:37:37.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-09-26 10:52:52.000000000 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2" ++#define MPFR_VERSION_STRING "3.1.2-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-03-13 15:37:34.000000000 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-09-26 10:52:52.000000000 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2"; ++ return "3.1.2-p1"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-09-26 10:56:55.000000000 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-09-26 10:56:55.000000000 +0000 +@@ -0,0 +1 @@ ++fits-smallneg +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-09-26 10:56:55.000000000 +0000 +@@ -1 +1 @@ +-3.1.2-p1 ++3.1.2-p2 +diff -Naurd mpfr-3.1.2-a/src/fits_u.h mpfr-3.1.2-b/src/fits_u.h +--- mpfr-3.1.2-a/src/fits_u.h 2013-03-13 15:37:35.000000000 +0000 ++++ mpfr-3.1.2-b/src/fits_u.h 2013-09-26 10:56:55.000000000 +0000 +@@ -32,17 +32,20 @@ + int res; + + if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (f))) +- /* Zero always fit */ +- return MPFR_IS_ZERO (f) ? 1 : 0; +- else if (MPFR_IS_NEG (f)) +- /* Negative numbers don't fit */ +- return 0; +- /* now it fits if +- (a) f <= MAXIMUM +- (b) round(f, prec(slong), rnd) <= MAXIMUM */ ++ return MPFR_IS_ZERO (f) ? 1 : 0; /* Zero always fits */ + + e = MPFR_GET_EXP (f); + ++ if (MPFR_IS_NEG (f)) ++ return e >= 1 ? 0 /* f <= -1 does not fit */ ++ : rnd != MPFR_RNDN ? MPFR_IS_LIKE_RNDU (rnd, -1) /* directed mode */ ++ : e < 0 ? 1 /* f > -1/2 fits in MPFR_RNDN */ ++ : mpfr_powerof2_raw(f); /* -1/2 fits, -1 < f < -1/2 don't */ ++ ++ /* Now it fits if ++ (a) f <= MAXIMUM ++ (b) round(f, prec(slong), rnd) <= MAXIMUM */ ++ + /* first compute prec(MAXIMUM); fits in an int */ + for (s = MAXIMUM, prec = 0; s != 0; s /= 2, prec ++); + +diff -Naurd mpfr-3.1.2-a/src/fits_uintmax.c mpfr-3.1.2-b/src/fits_uintmax.c +--- mpfr-3.1.2-a/src/fits_uintmax.c 2013-03-13 15:37:33.000000000 +0000 ++++ mpfr-3.1.2-b/src/fits_uintmax.c 2013-09-26 10:56:55.000000000 +0000 +@@ -27,51 +27,19 @@ + #include "mpfr-intmax.h" + #include "mpfr-impl.h" + +-#ifdef _MPFR_H_HAVE_INTMAX_T +- +-/* We can't use fits_u.h <= mpfr_cmp_ui */ +-int +-mpfr_fits_uintmax_p (mpfr_srcptr f, mpfr_rnd_t rnd) +-{ +- mpfr_exp_t e; +- int prec; +- uintmax_t s; +- mpfr_t x; +- int res; +- +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (f))) +- /* Zero always fit */ +- return MPFR_IS_ZERO (f) ? 1 : 0; +- else if (MPFR_IS_NEG (f)) +- /* Negative numbers don't fit */ +- return 0; +- /* now it fits if +- (a) f <= MAXIMUM +- (b) round(f, prec(slong), rnd) <= MAXIMUM */ +- +- e = MPFR_GET_EXP (f); +- +- /* first compute prec(MAXIMUM); fits in an int */ +- for (s = MPFR_UINTMAX_MAX, prec = 0; s != 0; s /= 2, prec ++); +- +- /* MAXIMUM needs prec bits, i.e. MAXIMUM = 2^prec - 1 */ +- +- /* if e <= prec - 1, then f < 2^(prec-1) < MAXIMUM */ +- if (e <= prec - 1) +- return 1; ++/* Note: though mpfr-impl.h is included in fits_u.h, we also include it ++ above so that it gets included even when _MPFR_H_HAVE_INTMAX_T is not ++ defined; this is necessary to avoid an empty translation unit, which ++ is forbidden by ISO C. Without this, a failing test can be reproduced ++ by creating an invalid stdint.h somewhere in the default include path ++ and by compiling MPFR with "gcc -ansi -pedantic-errors". */ + +- /* if e >= prec + 1, then f >= 2^prec > MAXIMUM */ +- if (e >= prec + 1) +- return 0; ++#ifdef _MPFR_H_HAVE_INTMAX_T + +- MPFR_ASSERTD (e == prec); ++#define FUNCTION mpfr_fits_uintmax_p ++#define MAXIMUM MPFR_UINTMAX_MAX ++#define TYPE uintmax_t + +- /* hard case: first round to prec bits, then check */ +- mpfr_init2 (x, prec); +- mpfr_set (x, f, rnd); +- res = MPFR_GET_EXP (x) == e; +- mpfr_clear (x); +- return res; +-} ++#include "fits_u.h" + + #endif +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-09-26 10:56:55.000000000 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p1" ++#define MPFR_VERSION_STRING "3.1.2-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-09-26 10:56:55.000000000 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p1"; ++ return "3.1.2-p2"; + } +diff -Naurd mpfr-3.1.2-a/tests/tfits.c mpfr-3.1.2-b/tests/tfits.c +--- mpfr-3.1.2-a/tests/tfits.c 2013-03-13 15:37:45.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tfits.c 2013-09-26 10:56:55.000000000 +0000 +@@ -33,155 +33,176 @@ + #include "mpfr-intmax.h" + #include "mpfr-test.h" + +-#define ERROR1 { printf("Initial error for x="); mpfr_dump(x); exit(1); } +-#define ERROR2 { printf("Error for x="); mpfr_dump(x); exit(1); } ++#define ERROR1(N) \ ++ do \ ++ { \ ++ printf("Error %d for rnd = %s and x = ", N, \ ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r)); \ ++ mpfr_dump(x); \ ++ exit(1); \ ++ } \ ++ while (0) + + static void check_intmax (void); + + int + main (void) + { +- mpfr_t x; ++ mpfr_t x, y; ++ int i, r; + + tests_start_mpfr (); + + mpfr_init2 (x, 256); ++ mpfr_init2 (y, 8); + +- /* Check NAN */ +- mpfr_set_nan (x); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR1; ++ RND_LOOP (r) ++ { + +- /* Check INF */ +- mpfr_set_inf (x, 1); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check NAN */ ++ mpfr_set_nan (x); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (1); ++ if (mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (2); ++ if (mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (3); ++ if (mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (4); ++ if (mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (5); ++ if (mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (6); + +- /* Check Zero */ +- MPFR_SET_ZERO (x); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check INF */ ++ mpfr_set_inf (x, 1); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (7); ++ if (mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (8); ++ if (mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (9); ++ if (mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (10); ++ if (mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (11); ++ if (mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (12); + +- /* Check small op */ +- mpfr_set_str1 (x, "1@-1"); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check Zero */ ++ MPFR_SET_ZERO (x); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (13); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (14); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (15); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (16); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (17); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (18); + +- /* Check 17 */ +- mpfr_set_ui (x, 17, MPFR_RNDN); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check small positive op */ ++ mpfr_set_str1 (x, "1@-1"); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (19); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (20); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (21); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (22); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (23); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (24); + +- /* Check all other values */ +- mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); +- mpfr_mul_2exp (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR1; +- mpfr_mul_2exp (x, x, 40, MPFR_RNDN); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check 17 */ ++ mpfr_set_ui (x, 17, MPFR_RNDN); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (25); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (26); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (27); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (28); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (29); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (30); + +- mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, LONG_MAX, MPFR_RNDN); +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, UINT_MAX, MPFR_RNDN); +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, INT_MAX, MPFR_RNDN); +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, USHRT_MAX, MPFR_RNDN); +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, SHRT_MAX, MPFR_RNDN); +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check all other values */ ++ mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); ++ mpfr_mul_2exp (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (31); ++ if (mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (32); ++ mpfr_mul_2exp (x, x, 40, MPFR_RNDN); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (33); ++ if (mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (34); ++ if (mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (35); ++ if (mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (36); ++ if (mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (37); + +- mpfr_set_si (x, 1, MPFR_RNDN); +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (38); ++ mpfr_set_ui (x, LONG_MAX, MPFR_RNDN); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (39); ++ mpfr_set_ui (x, UINT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (40); ++ mpfr_set_ui (x, INT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (41); ++ mpfr_set_ui (x, USHRT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (42); ++ mpfr_set_ui (x, SHRT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (43); + +- /* Check negative value */ +- mpfr_set_si (x, -1, MPFR_RNDN); +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; ++ mpfr_set_si (x, 1, MPFR_RNDN); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (44); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (45); ++ ++ /* Check negative op */ ++ for (i = 1; i <= 4; i++) ++ { ++ int inv; ++ ++ mpfr_set_si_2exp (x, -i, -2, MPFR_RNDN); ++ mpfr_rint (y, x, (mpfr_rnd_t) r); ++ inv = MPFR_NOTZERO (y); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (46); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (47); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (48); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (49); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (50); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (51); ++ } ++ } + + mpfr_clear (x); ++ mpfr_clear (y); + + check_intmax (); + +@@ -189,85 +210,98 @@ + return 0; + } + +-static void check_intmax (void) ++static void ++check_intmax (void) + { + #ifdef _MPFR_H_HAVE_INTMAX_T +- mpfr_t x; ++ mpfr_t x, y; ++ int i, r; + +- mpfr_init2 (x, sizeof (uintmax_t)*CHAR_BIT); ++ mpfr_init2 (x, sizeof (uintmax_t) * CHAR_BIT); ++ mpfr_init2 (y, 8); + +- /* Check NAN */ +- mpfr_set_nan (x); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ RND_LOOP (r) ++ { ++ /* Check NAN */ ++ mpfr_set_nan (x); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (52); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (53); + +- /* Check INF */ +- mpfr_set_inf (x, 1); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check INF */ ++ mpfr_set_inf (x, 1); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (54); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (55); + +- /* Check Zero */ +- MPFR_SET_ZERO (x); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check Zero */ ++ MPFR_SET_ZERO (x); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (56); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (57); + +- /* Check small op */ +- mpfr_set_str1 (x, "1@-1"); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check positive small op */ ++ mpfr_set_str1 (x, "1@-1"); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (58); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (59); + +- /* Check 17 */ +- mpfr_set_ui (x, 17, MPFR_RNDN); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check 17 */ ++ mpfr_set_ui (x, 17, MPFR_RNDN); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (60); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (61); + +- /* Check hugest */ +- mpfr_set_ui_2exp (x, 42, sizeof (uintmax_t) * 32, MPFR_RNDN); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check hugest */ ++ mpfr_set_ui_2exp (x, 42, sizeof (uintmax_t) * 32, MPFR_RNDN); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (62); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (63); + +- /* Check all other values */ +- mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); +- mpfr_add_ui (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); +- mpfr_add_ui (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; +- mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_sj (x, MPFR_INTMAX_MIN, MPFR_RNDN); +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_sub_ui (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check all other values */ ++ mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); ++ mpfr_add_ui (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (64); ++ mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (65); ++ mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); ++ mpfr_add_ui (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (66); ++ mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (67); ++ mpfr_set_sj (x, MPFR_INTMAX_MIN, MPFR_RNDN); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (68); ++ mpfr_sub_ui (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (69); + +- /* Check negative value */ +- mpfr_set_si (x, -1, MPFR_RNDN); +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check negative op */ ++ for (i = 1; i <= 4; i++) ++ { ++ int inv; ++ ++ mpfr_set_si_2exp (x, -i, -2, MPFR_RNDN); ++ mpfr_rint (y, x, (mpfr_rnd_t) r); ++ inv = MPFR_NOTZERO (y); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (70); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (71); ++ } ++ } + + mpfr_clear (x); ++ mpfr_clear (y); + #endif + } +- +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-10-09 13:34:21.000000000 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-10-09 13:34:21.000000000 +0000 +@@ -0,0 +1 @@ ++clang-divby0 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-10-09 13:34:21.000000000 +0000 +@@ -1 +1 @@ +-3.1.2-p2 ++3.1.2-p3 +diff -Naurd mpfr-3.1.2-a/src/mpfr-impl.h mpfr-3.1.2-b/src/mpfr-impl.h +--- mpfr-3.1.2-a/src/mpfr-impl.h 2013-03-13 15:37:36.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr-impl.h 2013-10-09 13:34:21.000000000 +0000 +@@ -468,8 +468,16 @@ + #define MPFR_LIMBS_PER_FLT ((IEEE_FLT_MANT_DIG-1)/GMP_NUMB_BITS+1) + + /* Visual C++ doesn't support +1.0/0.0, -1.0/0.0 and 0.0/0.0 +- at compile time. */ +-#if defined(_MSC_VER) && defined(_WIN32) && (_MSC_VER >= 1200) ++ at compile time. ++ Clang with -fsanitize=undefined is a bit similar due to a bug: ++ http://llvm.org/bugs/show_bug.cgi?id=17381 ++ but even without its sanitizer, it may be better to use the ++ double_zero version until IEEE 754 division by zero is properly ++ supported: ++ http://llvm.org/bugs/show_bug.cgi?id=17000 ++*/ ++#if (defined(_MSC_VER) && defined(_WIN32) && (_MSC_VER >= 1200)) || \ ++ defined(__clang__) + static double double_zero = 0.0; + # define DBL_NAN (double_zero/double_zero) + # define DBL_POS_INF ((double) 1.0/double_zero) +@@ -501,6 +509,8 @@ + (with Xcode 2.4.1, i.e. the latest one). */ + #define LVALUE(x) (&(x) == &(x) || &(x) != &(x)) + #define DOUBLE_ISINF(x) (LVALUE(x) && ((x) > DBL_MAX || (x) < -DBL_MAX)) ++/* The DOUBLE_ISNAN(x) macro is also valid on long double x ++ (assuming that the compiler isn't too broken). */ + #ifdef MPFR_NANISNAN + /* Avoid MIPSpro / IRIX64 / gcc -ffast-math (incorrect) optimizations. + The + must not be replaced by a ||. With gcc -ffast-math, NaN is +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-10-09 13:34:21.000000000 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p2" ++#define MPFR_VERSION_STRING "3.1.2-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-10-09 13:34:21.000000000 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p2"; ++ return "3.1.2-p3"; + } +diff -Naurd mpfr-3.1.2-a/tests/tget_flt.c mpfr-3.1.2-b/tests/tget_flt.c +--- mpfr-3.1.2-a/tests/tget_flt.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tget_flt.c 2013-10-09 13:34:21.000000000 +0000 +@@ -28,9 +28,17 @@ + main (void) + { + mpfr_t x, y; +- float f, g, infp; ++ float f, g; + int i; ++#if !defined(MPFR_ERRDIVZERO) ++ float infp; ++#endif ++ ++ tests_start_mpfr (); + ++#if !defined(MPFR_ERRDIVZERO) ++ /* The definition of DBL_POS_INF involves a division by 0. This makes ++ "clang -O2 -fsanitize=undefined -fno-sanitize-recover" fail. */ + infp = (float) DBL_POS_INF; + if (infp * 0.5 != infp) + { +@@ -38,8 +46,7 @@ + fprintf (stderr, "(this is probably a compiler bug, please report)\n"); + exit (1); + } +- +- tests_start_mpfr (); ++#endif + + mpfr_init2 (x, 24); + mpfr_init2 (y, 24); +@@ -353,6 +360,7 @@ + printf ("expected %.8e, got %.8e\n", g, f); + exit (1); + } ++#if !defined(MPFR_ERRDIVZERO) + f = mpfr_get_flt (x, MPFR_RNDN); /* first round to 2^128 (even rule), + thus we should get +Inf */ + g = infp; +@@ -376,6 +384,7 @@ + printf ("expected %.8e, got %.8e\n", g, f); + exit (1); + } ++#endif + + mpfr_clear (x); + mpfr_clear (y); +diff -Naurd mpfr-3.1.2-a/tests/tset_ld.c mpfr-3.1.2-b/tests/tset_ld.c +--- mpfr-3.1.2-a/tests/tset_ld.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tset_ld.c 2013-10-09 13:34:21.000000000 +0000 +@@ -47,8 +47,11 @@ + static int + Isnan_ld (long double d) + { +- double e = (double) d; +- if (DOUBLE_ISNAN (e)) ++ /* Do not convert d to double as this can give an overflow, which ++ may confuse compilers without IEEE 754 support (such as clang ++ -fsanitize=undefined), or trigger a trap if enabled. ++ The DOUBLE_ISNAN macro should work fine on long double. */ ++ if (DOUBLE_ISNAN (d)) + return 1; + LONGDOUBLE_NAN_ACTION (d, goto yes); + return 0; +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-11-15 00:51:49.323334999 +0000 +@@ -0,0 +1 @@ ++printf-alt0 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-11-15 00:51:49.323334999 +0000 +@@ -1 +1 @@ +-3.1.2-p3 ++3.1.2-p4 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-11-15 00:51:49.323334999 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p3" ++#define MPFR_VERSION_STRING "3.1.2-p4" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/vasprintf.c mpfr-3.1.2-b/src/vasprintf.c +--- mpfr-3.1.2-a/src/vasprintf.c 2013-03-13 15:37:37.000000000 +0000 ++++ mpfr-3.1.2-b/src/vasprintf.c 2013-11-15 00:51:49.267334408 +0000 +@@ -1040,7 +1040,7 @@ + } + + /* Determine the different parts of the string representation of the regular +- number P when SPEC.SPEC is 'e', 'E', 'g', or 'G'. ++ number P when spec.spec is 'e', 'E', 'g', or 'G'. + DEC_INFO contains the previously computed exponent and string or is NULL. + + return -1 if some field > INT_MAX */ +@@ -1167,7 +1167,7 @@ + } + + /* Determine the different parts of the string representation of the regular +- number P when SPEC.SPEC is 'f', 'F', 'g', or 'G'. ++ number P when spec.spec is 'f', 'F', 'g', or 'G'. + DEC_INFO contains the previously computed exponent and string or is NULL. + + return -1 if some field of number_parts is greater than INT_MAX */ +@@ -1559,7 +1559,7 @@ + /* fractional part */ + { + np->point = MPFR_DECIMAL_POINT; +- np->fp_trailing_zeros = (spec.spec == 'g' && spec.spec == 'G') ? ++ np->fp_trailing_zeros = (spec.spec == 'g' || spec.spec == 'G') ? + spec.prec - 1 : spec.prec; + } + else if (spec.alt) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-11-15 00:51:49.323334999 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p3"; ++ return "3.1.2-p4"; + } +diff -Naurd mpfr-3.1.2-a/tests/tsprintf.c mpfr-3.1.2-b/tests/tsprintf.c +--- mpfr-3.1.2-a/tests/tsprintf.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tsprintf.c 2013-11-15 00:51:49.267334408 +0000 +@@ -456,10 +456,16 @@ + check_sprintf ("1.999900 ", "%-#10.7RG", x); + check_sprintf ("1.9999 ", "%-10.7RG", x); + mpfr_set_ui (x, 1, MPFR_RNDN); ++ check_sprintf ("1.", "%#.1Rg", x); ++ check_sprintf ("1. ", "%-#5.1Rg", x); ++ check_sprintf (" 1.0", "%#5.2Rg", x); + check_sprintf ("1.00000000000000000000000000000", "%#.30Rg", x); + check_sprintf ("1", "%.30Rg", x); + mpfr_set_ui (x, 0, MPFR_RNDN); +- check_sprintf ("0.000000000000000000000000000000", "%#.30Rg", x); ++ check_sprintf ("0.", "%#.1Rg", x); ++ check_sprintf ("0. ", "%-#5.1Rg", x); ++ check_sprintf (" 0.0", "%#5.2Rg", x); ++ check_sprintf ("0.00000000000000000000000000000", "%#.30Rg", x); + check_sprintf ("0", "%.30Rg", x); + + /* following tests with precision 53 bits */ +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-12-01 11:07:49.575329762 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-12-01 11:07:49.751331625 +0000 +@@ -0,0 +1 @@ ++custom_init_set +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-12-01 11:07:49.571329714 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-12-01 11:07:49.747331585 +0000 +@@ -1 +1 @@ +-3.1.2-p4 ++3.1.2-p5 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-12-01 11:07:49.571329714 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-12-01 11:07:49.747331585 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p4" ++#define MPFR_VERSION_STRING "3.1.2-p5" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +@@ -861,7 +861,7 @@ + _t = (mpfr_kind_t) _k; \ + _s = 1; \ + } else { \ +- _t = (mpfr_kind_t) -k; \ ++ _t = (mpfr_kind_t) - _k; \ + _s = -1; \ + } \ + _e = _t == MPFR_REGULAR_KIND ? (e) : \ +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-12-01 11:07:49.575329762 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-12-01 11:07:49.747331585 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p4"; ++ return "3.1.2-p5"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-04-15 21:56:49.697059857 +0000 +@@ -0,0 +1 @@ ++li2-return +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-04-15 21:56:49.697059857 +0000 +@@ -1 +1 @@ +-3.1.2-p5 ++3.1.2-p6 +diff -Naurd mpfr-3.1.2-a/src/li2.c mpfr-3.1.2-b/src/li2.c +--- mpfr-3.1.2-a/src/li2.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/li2.c 2014-04-15 21:56:49.653058661 +0000 +@@ -630,5 +630,5 @@ + return mpfr_check_range (y, inexact, rnd_mode); + } + +- MPFR_ASSERTN (0); /* should never reach this point */ ++ MPFR_RET_NEVER_GO_HERE (); + } +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-04-15 21:56:49.697059857 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p5" ++#define MPFR_VERSION_STRING "3.1.2-p6" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-04-15 21:56:49.697059857 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p5"; ++ return "3.1.2-p6"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-04-15 22:04:57.090286262 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-04-15 22:04:57.162288198 +0000 +@@ -0,0 +1 @@ ++exp3 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-04-15 22:04:57.086286154 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-04-15 22:04:57.162288198 +0000 +@@ -1 +1 @@ +-3.1.2-p6 ++3.1.2-p7 +diff -Naurd mpfr-3.1.2-a/src/exp3.c mpfr-3.1.2-b/src/exp3.c +--- mpfr-3.1.2-a/src/exp3.c 2013-03-13 15:37:34.000000000 +0000 ++++ mpfr-3.1.2-b/src/exp3.c 2014-04-15 22:04:57.126287230 +0000 +@@ -283,7 +283,7 @@ + } + } + +- if (mpfr_can_round (shift_x > 0 ? t : tmp, realprec, MPFR_RNDD, MPFR_RNDZ, ++ if (mpfr_can_round (shift_x > 0 ? t : tmp, realprec, MPFR_RNDN, MPFR_RNDZ, + MPFR_PREC(y) + (rnd_mode == MPFR_RNDN))) + { + inexact = mpfr_set (y, shift_x > 0 ? t : tmp, rnd_mode); +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-04-15 22:04:57.086286154 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-04-15 22:04:57.162288198 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p6" ++#define MPFR_VERSION_STRING "3.1.2-p7" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-04-15 22:04:57.090286262 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-04-15 22:04:57.162288198 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p6"; ++ return "3.1.2-p7"; + } +diff -Naurd mpfr-3.1.2-a/tests/texp.c mpfr-3.1.2-b/tests/texp.c +--- mpfr-3.1.2-a/tests/texp.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/texp.c 2014-04-15 22:04:57.126287230 +0000 +@@ -150,6 +150,22 @@ + exit (1); + } + ++ mpfr_set_prec (x, 118); ++ mpfr_set_str_binary (x, "0.1110010100011101010000111110011000000000000000000000000000000000000000000000000000000000000000000000000000000000000000E-86"); ++ mpfr_set_prec (y, 118); ++ mpfr_exp_2 (y, x, MPFR_RNDU); ++ mpfr_exp_3 (x, x, MPFR_RNDU); ++ if (mpfr_cmp (x, y)) ++ { ++ printf ("mpfr_exp_2 and mpfr_exp_3 differ for prec=118\n"); ++ printf ("mpfr_exp_2 gives "); ++ mpfr_out_str (stdout, 2, 0, y, MPFR_RNDN); ++ printf ("\nmpfr_exp_3 gives "); ++ mpfr_out_str (stdout, 2, 0, x, MPFR_RNDN); ++ printf ("\n"); ++ exit (1); ++ } ++ + mpfr_clear (x); + mpfr_clear (y); + return 0; +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-04-15 22:20:32.243481506 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-04-15 22:22:32.418722707 +0000 +@@ -0,0 +1 @@ ++gmp6-compat +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-04-15 22:20:20.755171478 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-04-15 22:21:45.225450147 +0000 +@@ -1 +1 @@ +-3.1.2-p7 ++3.1.2-p8 +diff -Naurd mpfr-3.1.2-a/configure mpfr-3.1.2-b/configure +--- mpfr-3.1.2-a/configure 2013-03-13 15:38:20.000000000 +0000 ++++ mpfr-3.1.2-b/configure 2014-04-15 22:21:38.821277476 +0000 +@@ -14545,26 +14545,30 @@ + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + fi + +-if test "$use_gmp_build" = yes ; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for valid GMP_NUMB_BITS" >&5 +-$as_echo_n "checking for valid GMP_NUMB_BITS... " >&6; } +- if test "$cross_compiling" = yes; then : ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency" >&5 ++$as_echo_n "checking for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency... " >&6; } ++if test "$cross_compiling" = yes; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: result: can't test" >&5 + $as_echo "can't test" >&6; } + else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + ++#include + #include + #include "gmp.h" +-#include "gmp-impl.h" + + int + main () + { + +- return GMP_NUMB_BITS == BYTES_PER_MP_LIMB * CHAR_BIT +- && sizeof(mp_limb_t) == BYTES_PER_MP_LIMB ? 0 : 1; ++ if (GMP_NUMB_BITS == sizeof(mp_limb_t) * CHAR_BIT) ++ return 0; ++ fprintf (stderr, "GMP_NUMB_BITS = %ld\n", (long) GMP_NUMB_BITS); ++ fprintf (stderr, "sizeof(mp_limb_t) = %ld\n", (long) sizeof(mp_limb_t)); ++ fprintf (stderr, "sizeof(mp_limb_t) * CHAR_BIT = %ld != GMP_NUMB_BITS\n", ++ (long) (sizeof(mp_limb_t) * CHAR_BIT)); ++ return 1; + + ; + return 0; +@@ -14577,14 +14581,14 @@ + + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "no" >&6; } +- as_fn_error $? "GMP_NUMB_BITS is incorrect. +-You probably need to change some of the GMP or MPFR compile options." "$LINENO" 5 ++ as_fn_error $? "GMP_NUMB_BITS and sizeof(mp_limb_t) are not consistent. ++You probably need to change some of the GMP or MPFR compile options. ++See 'config.log' for details (search for GMP_NUMB_BITS)." "$LINENO" 5 + fi + rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ + conftest.$ac_objext conftest.beam conftest.$ac_ext + fi + +-fi + + + if test "$dont_link_with_gmp" = yes ; then +diff -Naurd mpfr-3.1.2-a/configure.ac mpfr-3.1.2-b/configure.ac +--- mpfr-3.1.2-a/configure.ac 2013-03-13 15:37:46.000000000 +0000 ++++ mpfr-3.1.2-b/configure.ac 2013-03-13 15:37:46.000000000 +0000 +@@ -435,23 +435,29 @@ + ]) + fi + +-dnl Check for valid GMP_NUMB_BITS and BYTES_PER_MP_LIMB ++dnl Check for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency. ++dnl Problems may occur if gmp.h was generated with some ABI ++dnl and is used with another ABI (or if nails are used). + dnl This test doesn't need to link with libgmp (at least it shouldn't). +-if test "$use_gmp_build" = yes ; then +- AC_MSG_CHECKING(for valid GMP_NUMB_BITS) +- AC_RUN_IFELSE([AC_LANG_PROGRAM([[ ++AC_MSG_CHECKING(for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency) ++AC_RUN_IFELSE([AC_LANG_PROGRAM([[ ++#include + #include + #include "gmp.h" +-#include "gmp-impl.h" + ]], [[ +- return GMP_NUMB_BITS == BYTES_PER_MP_LIMB * CHAR_BIT +- && sizeof(mp_limb_t) == BYTES_PER_MP_LIMB ? 0 : 1; ++ if (GMP_NUMB_BITS == sizeof(mp_limb_t) * CHAR_BIT) ++ return 0; ++ fprintf (stderr, "GMP_NUMB_BITS = %ld\n", (long) GMP_NUMB_BITS); ++ fprintf (stderr, "sizeof(mp_limb_t) = %ld\n", (long) sizeof(mp_limb_t)); ++ fprintf (stderr, "sizeof(mp_limb_t) * CHAR_BIT = %ld != GMP_NUMB_BITS\n", ++ (long) (sizeof(mp_limb_t) * CHAR_BIT)); ++ return 1; + ]])], [AC_MSG_RESULT(yes)], [ + AC_MSG_RESULT(no) +- AC_MSG_ERROR([GMP_NUMB_BITS is incorrect. +-You probably need to change some of the GMP or MPFR compile options.])], ++ AC_MSG_ERROR([GMP_NUMB_BITS and sizeof(mp_limb_t) are not consistent. ++You probably need to change some of the GMP or MPFR compile options. ++See 'config.log' for details (search for GMP_NUMB_BITS).])], + [AC_MSG_RESULT([can't test])]) +-fi + + + dnl We really need to link using libtool. But it is impossible with the current +diff -Naurd mpfr-3.1.2-a/src/init2.c mpfr-3.1.2-b/src/init2.c +--- mpfr-3.1.2-a/src/init2.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/init2.c 2014-04-15 22:21:06.220398489 +0000 +@@ -30,11 +30,11 @@ + + /* Check if we can represent the number of limbs + * associated to the maximum of mpfr_prec_t*/ +- MPFR_ASSERTN( MP_SIZE_T_MAX >= (MPFR_PREC_MAX/BYTES_PER_MP_LIMB) ); ++ MPFR_ASSERTN( MP_SIZE_T_MAX >= (MPFR_PREC_MAX/MPFR_BYTES_PER_MP_LIMB) ); + +- /* Check for correct GMP_NUMB_BITS and BYTES_PER_MP_LIMB */ +- MPFR_ASSERTN( GMP_NUMB_BITS == BYTES_PER_MP_LIMB * CHAR_BIT +- && sizeof(mp_limb_t) == BYTES_PER_MP_LIMB ); ++ /* Check for correct GMP_NUMB_BITS and MPFR_BYTES_PER_MP_LIMB */ ++ MPFR_ASSERTN( GMP_NUMB_BITS == MPFR_BYTES_PER_MP_LIMB * CHAR_BIT ++ && sizeof(mp_limb_t) == MPFR_BYTES_PER_MP_LIMB ); + + MPFR_ASSERTN (mp_bits_per_limb == GMP_NUMB_BITS); + +diff -Naurd mpfr-3.1.2-a/src/mpfr-gmp.h mpfr-3.1.2-b/src/mpfr-gmp.h +--- mpfr-3.1.2-a/src/mpfr-gmp.h 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr-gmp.h 2014-04-15 22:21:06.220398489 +0000 +@@ -72,7 +72,6 @@ + #endif + + /* Define some macros */ +-#define BYTES_PER_MP_LIMB (GMP_NUMB_BITS/CHAR_BIT) + + #define MP_LIMB_T_MAX (~(mp_limb_t)0) + +@@ -96,19 +95,19 @@ + #define SHRT_HIGHBIT SHRT_MIN + + /* MP_LIMB macros */ +-#define MPN_ZERO(dst, n) memset((dst), 0, (n)*BYTES_PER_MP_LIMB) +-#define MPN_COPY_DECR(dst,src,n) memmove((dst),(src),(n)*BYTES_PER_MP_LIMB) +-#define MPN_COPY_INCR(dst,src,n) memmove((dst),(src),(n)*BYTES_PER_MP_LIMB) ++#define MPN_ZERO(dst, n) memset((dst), 0, (n)*MPFR_BYTES_PER_MP_LIMB) ++#define MPN_COPY_DECR(dst,src,n) memmove((dst),(src),(n)*MPFR_BYTES_PER_MP_LIMB) ++#define MPN_COPY_INCR(dst,src,n) memmove((dst),(src),(n)*MPFR_BYTES_PER_MP_LIMB) + #define MPN_COPY(dst,src,n) \ + do \ + { \ + if ((dst) != (src)) \ + { \ + MPFR_ASSERTD ((char *) (dst) >= (char *) (src) + \ +- (n) * BYTES_PER_MP_LIMB || \ ++ (n) * MPFR_BYTES_PER_MP_LIMB || \ + (char *) (src) >= (char *) (dst) + \ +- (n) * BYTES_PER_MP_LIMB); \ +- memcpy ((dst), (src), (n) * BYTES_PER_MP_LIMB); \ ++ (n) * MPFR_BYTES_PER_MP_LIMB); \ ++ memcpy ((dst), (src), (n) * MPFR_BYTES_PER_MP_LIMB); \ + } \ + } \ + while (0) +diff -Naurd mpfr-3.1.2-a/src/mpfr-impl.h mpfr-3.1.2-b/src/mpfr-impl.h +--- mpfr-3.1.2-a/src/mpfr-impl.h 2013-10-09 13:34:21.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr-impl.h 2014-04-15 22:21:06.220398489 +0000 +@@ -191,7 +191,7 @@ + # endif + #endif + +- ++#define MPFR_BYTES_PER_MP_LIMB (GMP_NUMB_BITS/CHAR_BIT) + + /****************************************************** + ******************** Check GMP *********************** +@@ -930,7 +930,7 @@ + #define MPFR_SET_ALLOC_SIZE(x, n) \ + ( ((mp_size_t*) MPFR_MANT(x))[-1] = n) + #define MPFR_MALLOC_SIZE(s) \ +- ( sizeof(mpfr_size_limb_t) + BYTES_PER_MP_LIMB * ((size_t) s) ) ++ ( sizeof(mpfr_size_limb_t) + MPFR_BYTES_PER_MP_LIMB * ((size_t) s) ) + #define MPFR_SET_MANT_PTR(x,p) \ + (MPFR_MANT(x) = (mp_limb_t*) ((mpfr_size_limb_t*) p + 1)) + #define MPFR_GET_REAL_PTR(x) \ +@@ -964,7 +964,7 @@ + #endif + + #define MPFR_TMP_LIMBS_ALLOC(N) \ +- ((mp_limb_t *) MPFR_TMP_ALLOC ((size_t) (N) * BYTES_PER_MP_LIMB)) ++ ((mp_limb_t *) MPFR_TMP_ALLOC ((size_t) (N) * MPFR_BYTES_PER_MP_LIMB)) + + /* temporary allocate 1 limb at xp, and initialize mpfr variable x */ + /* The temporary var doesn't have any size field, but it doesn't matter +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-04-15 22:20:20.755171478 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-04-15 22:21:45.225450147 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p7" ++#define MPFR_VERSION_STRING "3.1.2-p8" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/mul.c mpfr-3.1.2-b/src/mul.c +--- mpfr-3.1.2-a/src/mul.c 2013-03-13 15:37:37.000000000 +0000 ++++ mpfr-3.1.2-b/src/mul.c 2014-04-15 22:21:06.224398597 +0000 +@@ -106,7 +106,7 @@ + MPFR_ASSERTD(tn <= k); + + /* Check for no size_t overflow*/ +- MPFR_ASSERTD((size_t) k <= ((size_t) -1) / BYTES_PER_MP_LIMB); ++ MPFR_ASSERTD((size_t) k <= ((size_t) -1) / MPFR_BYTES_PER_MP_LIMB); + MPFR_TMP_MARK(marker); + tmp = MPFR_TMP_LIMBS_ALLOC (k); + +@@ -301,7 +301,7 @@ + MPFR_ASSERTD (tn <= k); /* tn <= k, thus no int overflow */ + + /* Check for no size_t overflow*/ +- MPFR_ASSERTD ((size_t) k <= ((size_t) -1) / BYTES_PER_MP_LIMB); ++ MPFR_ASSERTD ((size_t) k <= ((size_t) -1) / MPFR_BYTES_PER_MP_LIMB); + MPFR_TMP_MARK (marker); + tmp = MPFR_TMP_LIMBS_ALLOC (k); + +diff -Naurd mpfr-3.1.2-a/src/stack_interface.c mpfr-3.1.2-b/src/stack_interface.c +--- mpfr-3.1.2-a/src/stack_interface.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/stack_interface.c 2014-04-15 22:21:06.220398489 +0000 +@@ -26,7 +26,7 @@ + size_t + mpfr_custom_get_size (mpfr_prec_t prec) + { +- return MPFR_PREC2LIMBS (prec) * BYTES_PER_MP_LIMB; ++ return MPFR_PREC2LIMBS (prec) * MPFR_BYTES_PER_MP_LIMB; + } + + #undef mpfr_custom_init +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-04-15 22:20:20.755171478 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-04-15 22:21:45.225450147 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p7"; ++ return "3.1.2-p8"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-06-30 15:15:25.533266905 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-06-30 15:15:25.617269178 +0000 +@@ -0,0 +1 @@ ++div-overflow +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-06-30 15:15:25.529266797 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-06-30 15:15:25.617269178 +0000 +@@ -1 +1 @@ +-3.1.2-p8 ++3.1.2-p9 +diff -Naurd mpfr-3.1.2-a/src/div.c mpfr-3.1.2-b/src/div.c +--- mpfr-3.1.2-a/src/div.c 2013-03-13 15:37:33.000000000 +0000 ++++ mpfr-3.1.2-b/src/div.c 2014-06-30 15:15:25.585268312 +0000 +@@ -750,7 +750,9 @@ + truncate_check_qh: + if (qh) + { +- qexp ++; ++ if (MPFR_LIKELY (qexp < MPFR_EXP_MAX)) ++ qexp ++; ++ /* else qexp is now incorrect, but one will still get an overflow */ + q0p[q0size - 1] = MPFR_LIMB_HIGHBIT; + } + goto truncate; +@@ -765,7 +767,9 @@ + inex = 1; /* always here */ + if (mpn_add_1 (q0p, q0p, q0size, MPFR_LIMB_ONE << sh)) + { +- qexp ++; ++ if (MPFR_LIKELY (qexp < MPFR_EXP_MAX)) ++ qexp ++; ++ /* else qexp is now incorrect, but one will still get an overflow */ + q0p[q0size - 1] = MPFR_LIMB_HIGHBIT; + } + +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-06-30 15:15:25.533266905 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-06-30 15:15:25.613269070 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p8" ++#define MPFR_VERSION_STRING "3.1.2-p9" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-06-30 15:15:25.533266905 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-06-30 15:15:25.613269070 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p8"; ++ return "3.1.2-p9"; + } +diff -Naurd mpfr-3.1.2-a/tests/tdiv.c mpfr-3.1.2-b/tests/tdiv.c +--- mpfr-3.1.2-a/tests/tdiv.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tdiv.c 2014-06-30 15:15:25.585268312 +0000 +@@ -1104,6 +1104,96 @@ + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) + #include "tgeneric.c" + ++static void ++test_extreme (void) ++{ ++ mpfr_t x, y, z; ++ mpfr_exp_t emin, emax; ++ mpfr_prec_t p[4] = { 8, 32, 64, 256 }; ++ int xi, yi, zi, j, r; ++ unsigned int flags, ex_flags; ++ ++ emin = mpfr_get_emin (); ++ emax = mpfr_get_emax (); ++ ++ mpfr_set_emin (MPFR_EMIN_MIN); ++ mpfr_set_emax (MPFR_EMAX_MAX); ++ ++ for (xi = 0; xi < 4; xi++) ++ { ++ mpfr_init2 (x, p[xi]); ++ mpfr_setmax (x, MPFR_EMAX_MAX); ++ MPFR_ASSERTN (mpfr_check (x)); ++ for (yi = 0; yi < 4; yi++) ++ { ++ mpfr_init2 (y, p[yi]); ++ mpfr_setmin (y, MPFR_EMIN_MIN); ++ for (j = 0; j < 2; j++) ++ { ++ MPFR_ASSERTN (mpfr_check (y)); ++ for (zi = 0; zi < 4; zi++) ++ { ++ mpfr_init2 (z, p[zi]); ++ RND_LOOP (r) ++ { ++ mpfr_clear_flags (); ++ mpfr_div (z, x, y, (mpfr_rnd_t) r); ++ flags = __gmpfr_flags; ++ MPFR_ASSERTN (mpfr_check (z)); ++ ex_flags = MPFR_FLAGS_OVERFLOW | MPFR_FLAGS_INEXACT; ++ if (flags != ex_flags) ++ { ++ printf ("Bad flags in test_extreme on z = a/b" ++ " with %s and\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r)); ++ printf ("a = "); ++ mpfr_dump (x); ++ printf ("b = "); ++ mpfr_dump (y); ++ printf ("Expected flags:"); ++ flags_out (ex_flags); ++ printf ("Got flags: "); ++ flags_out (flags); ++ printf ("z = "); ++ mpfr_dump (z); ++ exit (1); ++ } ++ mpfr_clear_flags (); ++ mpfr_div (z, y, x, (mpfr_rnd_t) r); ++ flags = __gmpfr_flags; ++ MPFR_ASSERTN (mpfr_check (z)); ++ ex_flags = MPFR_FLAGS_UNDERFLOW | MPFR_FLAGS_INEXACT; ++ if (flags != ex_flags) ++ { ++ printf ("Bad flags in test_extreme on z = a/b" ++ " with %s and\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r)); ++ printf ("a = "); ++ mpfr_dump (y); ++ printf ("b = "); ++ mpfr_dump (x); ++ printf ("Expected flags:"); ++ flags_out (ex_flags); ++ printf ("Got flags: "); ++ flags_out (flags); ++ printf ("z = "); ++ mpfr_dump (z); ++ exit (1); ++ } ++ } ++ mpfr_clear (z); ++ } /* zi */ ++ mpfr_nextabove (y); ++ } /* j */ ++ mpfr_clear (y); ++ } /* yi */ ++ mpfr_clear (x); ++ } /* xi */ ++ ++ set_emin (emin); ++ set_emax (emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1130,6 +1220,7 @@ + test_20070603 (); + test_20070628 (); + test_generic (2, 800, 50); ++ test_extreme (); + + tests_end_mpfr (); + return 0; +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-06-30 15:17:53.417270314 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-06-30 15:17:53.413270206 +0000 +@@ -1 +1 @@ +-3.1.2-p9 ++3.1.2-p10 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-06-30 15:17:53.413270206 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p9" ++#define MPFR_VERSION_STRING "3.1.2-p10" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/vasprintf.c mpfr-3.1.2-b/src/vasprintf.c +--- mpfr-3.1.2-a/src/vasprintf.c 2013-11-15 00:51:49.267334408 +0000 ++++ mpfr-3.1.2-b/src/vasprintf.c 2014-06-30 15:17:53.377269231 +0000 +@@ -884,14 +884,18 @@ + first digit, we want the exponent for radix two and the decimal + point AFTER the first digit. */ + { +- MPFR_ASSERTN (exp > MPFR_EMIN_MIN /4); /* possible overflow */ ++ /* An integer overflow is normally not possible since MPFR_EXP_MIN ++ is twice as large as MPFR_EMIN_MIN. */ ++ MPFR_ASSERTN (exp > (MPFR_EXP_MIN + 3) / 4); + exp = (exp - 1) * 4; + } + else + /* EXP is the exponent for decimal point BEFORE the first digit, we + want the exponent for decimal point AFTER the first digit. */ + { +- MPFR_ASSERTN (exp > MPFR_EMIN_MIN); /* possible overflow */ ++ /* An integer overflow is normally not possible since MPFR_EXP_MIN ++ is twice as large as MPFR_EMIN_MIN. */ ++ MPFR_ASSERTN (exp > MPFR_EXP_MIN); + --exp; + } + } +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-06-30 15:17:53.413270206 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p9"; ++ return "3.1.2-p10"; + } +diff -Naurd mpfr-3.1.2-a/tests/tsprintf.c mpfr-3.1.2-b/tests/tsprintf.c +--- mpfr-3.1.2-a/tests/tsprintf.c 2013-11-15 00:51:49.267334408 +0000 ++++ mpfr-3.1.2-b/tests/tsprintf.c 2014-06-30 15:17:53.377269231 +0000 +@@ -1184,6 +1184,69 @@ + check_emax_aux (MPFR_EMAX_MAX); + } + ++static void ++check_emin_aux (mpfr_exp_t e) ++{ ++ mpfr_t x; ++ char *s1, s2[256]; ++ int i; ++ mpfr_exp_t emin; ++ mpz_t ee; ++ ++ MPFR_ASSERTN (e >= LONG_MIN); ++ emin = mpfr_get_emin (); ++ set_emin (e); ++ ++ mpfr_init2 (x, 16); ++ mpz_init (ee); ++ ++ mpfr_setmin (x, e); ++ mpz_set_si (ee, e); ++ mpz_sub_ui (ee, ee, 1); ++ ++ i = mpfr_asprintf (&s1, "%Ra", x); ++ MPFR_ASSERTN (i > 0); ++ ++ gmp_snprintf (s2, 256, "0x1p%Zd", ee); ++ ++ if (strcmp (s1, s2) != 0) ++ { ++ printf ("Error in check_emin_aux for emin = %ld\n", (long) e); ++ printf ("Expected %s\n", s2); ++ printf ("Got %s\n", s1); ++ exit (1); ++ } ++ ++ mpfr_free_str (s1); ++ ++ i = mpfr_asprintf (&s1, "%Rb", x); ++ MPFR_ASSERTN (i > 0); ++ ++ gmp_snprintf (s2, 256, "1p%Zd", ee); ++ ++ if (strcmp (s1, s2) != 0) ++ { ++ printf ("Error in check_emin_aux for emin = %ld\n", (long) e); ++ printf ("Expected %s\n", s2); ++ printf ("Got %s\n", s1); ++ exit (1); ++ } ++ ++ mpfr_free_str (s1); ++ ++ mpfr_clear (x); ++ mpz_clear (ee); ++ set_emin (emin); ++} ++ ++static void ++check_emin (void) ++{ ++ check_emin_aux (-15); ++ check_emin_aux (mpfr_get_emin ()); ++ check_emin_aux (MPFR_EMIN_MIN); ++} ++ + int + main (int argc, char **argv) + { +@@ -1203,6 +1266,7 @@ + decimal (); + mixed (); + check_emax (); ++ check_emin (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + locale_da_DK (); +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-12-04 01:41:57.131789485 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-12-04 01:41:57.339791833 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-12-04 01:41:57.127789443 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-12-04 01:41:57.339791833 +0000 +@@ -1 +1 @@ +-3.1.2-p10 ++3.1.2-p11 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-12-04 01:41:57.127789443 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-12-04 01:41:57.335791790 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p10" ++#define MPFR_VERSION_STRING "3.1.2-p11" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/strtofr.c mpfr-3.1.2-b/src/strtofr.c +--- mpfr-3.1.2-a/src/strtofr.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/strtofr.c 2014-12-04 01:41:57.287791246 +0000 +@@ -473,8 +473,10 @@ + /* prec bits corresponds to ysize limbs */ + ysize_bits = ysize * GMP_NUMB_BITS; + /* and to ysize_bits >= prec > MPFR_PREC (x) bits */ +- y = MPFR_TMP_LIMBS_ALLOC (2 * ysize + 1); +- y += ysize; /* y has (ysize+1) allocated limbs */ ++ /* we need to allocate one more limb to work around bug ++ https://gmplib.org/list-archives/gmp-bugs/2013-December/003267.html */ ++ y = MPFR_TMP_LIMBS_ALLOC (2 * ysize + 2); ++ y += ysize; /* y has (ysize+2) allocated limbs */ + + /* pstr_size is the number of characters we read in pstr->mant + to have at least ysize full limbs. +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-12-04 01:41:57.131789485 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-12-04 01:41:57.339791833 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p10"; ++ return "3.1.2-p11"; + } -- GitLab From 2aa2adf21c052863684bdcf72ca43b3d0d8225d9 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 13 Apr 2015 15:57:08 +0200 Subject: [PATCH 245/992] Support Spark 1.3.0 --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 26 ++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb new file mode 100644 index 0000000000..7f97113c7d --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '1.3.0' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] +source_urls = ['http://www.apache.org/dyn/closer.cgi/spark/%(namelower)s-%(version)s'] + +java = 'Java' +javaver = '1.7.0_40' + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['bin', 'lib', 'python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' -- GitLab From 404cce4fa83211c0b592fa7694fd9cf33b297006 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 14 Apr 2015 13:55:22 +0200 Subject: [PATCH 246/992] added easyconfig for newer mathematica versions --- .../m/Mathematica/Mathematica-10.0.2.eb | 14 ++++++++++++++ .../m/Mathematica/Mathematica-10.1.0.eb | 14 ++++++++++++++ 2 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb new file mode 100644 index 0000000000..cb33bf4bb0 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '10.0.2' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%s_LINUX.sh' % version] + +license_server = 'license.example.com' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb new file mode 100644 index 0000000000..79b9255141 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '10.1.0' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%s_LINUX.sh' % version] + +license_server = 'license.example.com' + +moduleclass = 'math' -- GitLab From bd259ad02ba9ce9b9e7380edd4f2f8e954190f80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Apr 2015 22:10:58 +0200 Subject: [PATCH 247/992] include fftw dep in Cray toolchains --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 2 ++ easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 2 ++ easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 2 ++ easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 2 ++ easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb | 2 ++ easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb | 2 ++ 6 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb index f09961bd60..45d88cae31 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.0')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb index ff0774c751..78c6b82ec4 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.2')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index d2d1520bce..f5228016b8 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.0')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index afc8c6010c..0577186f67 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.2')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb index 6cb4679750..9f906e92b4 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.0')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb index f24f574b3f..bcd630f2e9 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.2')] + moduleclass = 'toolchain' -- GitLab From e70bb2853bdde3680953ea2038fbc6507cfd6f18 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 20 Apr 2015 13:27:21 +0200 Subject: [PATCH 248/992] Remove check of bin dir since we check a file in bin anyway. --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index 7f97113c7d..5c8d510430 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -18,7 +18,7 @@ dependencies = [(java, javaver)] sanity_check_paths = { 'files': ['bin/spark-shell'], - 'dirs': ['bin', 'lib', 'python'] + 'dirs': ['lib', 'python'] } modextrapaths = {'PYTHONPATH': 'python'} -- GitLab From 9c618b599a4aae422aa055285ee02d41f078baf9 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 20 Apr 2015 13:57:17 +0200 Subject: [PATCH 249/992] Update java dep version. --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index 5c8d510430..4a9f913b52 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -12,7 +12,7 @@ sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] source_urls = ['http://www.apache.org/dyn/closer.cgi/spark/%(namelower)s-%(version)s'] java = 'Java' -javaver = '1.7.0_40' +javaver = '1.7.0_76' dependencies = [(java, javaver)] -- GitLab From 4359a869a93472ebaceb82bd0298f2dd424bb0f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 14:13:00 +0200 Subject: [PATCH 250/992] collapse deps --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index 4a9f913b52..d635db080f 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -11,10 +11,7 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] source_urls = ['http://www.apache.org/dyn/closer.cgi/spark/%(namelower)s-%(version)s'] -java = 'Java' -javaver = '1.7.0_76' - -dependencies = [(java, javaver)] +dependencies = [('Java', '1.7.0_76')] sanity_check_paths = { 'files': ['bin/spark-shell'], -- GitLab From 4bd6b21cf3ef92004b71798ced797cce9e455f1a Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 20 Apr 2015 15:09:09 +0200 Subject: [PATCH 251/992] Fix sources. --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index 4a9f913b52..15aa2288da 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -9,7 +9,11 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] -source_urls = ['http://www.apache.org/dyn/closer.cgi/spark/%(namelower)s-%(version)s'] +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] java = 'Java' javaver = '1.7.0_76' -- GitLab From 288967c089c19a8599a71336b858fc40b79f049f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 16:12:00 +0200 Subject: [PATCH 252/992] include petsc_arch spec in SLEPc 3.5.3 easyconfig --- .../easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb index 2253b31148..0f01678e28 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -16,4 +16,6 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('PETSc', '3.5.3', versionsuffix)] +petsc_arch = 'arch-linux2-c-opt' + moduleclass = 'numlib' -- GitLab From 5c18bb7e6a8b9198c2ce892b271cc6c86465f916 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 16:33:31 +0200 Subject: [PATCH 253/992] fix remarks --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb | 2 +- easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb index ef2bf9ff97..cea8ae91c9 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb @@ -17,6 +17,6 @@ source_urls = [ patches = ['METIS_IDXTYPEWIDTH.patch'] -builddependencies = [('CMake', '3.0.0')] +builddependencies = [('CMake', '3.2.1')] moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch index 363f95c19f..0689e81b9f 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch @@ -1,3 +1,5 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) diff -ur numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py --- numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py 2014-03-25 20:43:24.000000000 +0100 +++ numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py 2014-07-08 15:22:31.471064031 +0200 -- GitLab From 73ead9e2d22f40790446a1b2ded92a34575693b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 16:35:34 +0200 Subject: [PATCH 254/992] use %(version)s template --- easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb | 2 +- easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb | 2 +- easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb | 2 +- easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch | 2 ++ 4 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb index cb33bf4bb0..e1bdcca9da 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb @@ -7,7 +7,7 @@ and computing fields.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['Mathematica_%s_LINUX.sh' % version] +sources = ['Mathematica_%(version)s_LINUX.sh'] license_server = 'license.example.com' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb index 79b9255141..0093f6a4c2 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb @@ -7,7 +7,7 @@ and computing fields.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['Mathematica_%s_LINUX.sh' % version] +sources = ['Mathematica_%(version)s_LINUX.sh'] license_server = 'license.example.com' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb index 2d148e7a75..aafd02cf83 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb @@ -7,7 +7,7 @@ and computing fields.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['Mathematica_%s_LINUX.sh' % version] +sources = ['Mathematica_%(version)s_LINUX.sh'] license_server = 'license.example.com' diff --git a/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch b/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch index 363f95c19f..0689e81b9f 100644 --- a/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch +++ b/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch @@ -1,3 +1,5 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) diff -ur numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py --- numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py 2014-03-25 20:43:24.000000000 +0100 +++ numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py 2014-07-08 15:22:31.471064031 +0200 -- GitLab From 4255429a0b3bd98bd547cfa009089c6a5ebe2da3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 17:41:51 +0200 Subject: [PATCH 255/992] add CMake as build dep to getdp/gmsh easyconfigs --- .../c/CMake/CMake-3.2.2-intel-2015a.eb | 22 +++++++++++++++++++ .../g/getdp/getdp-2.5.0-intel-2015a.eb | 2 ++ .../g/gmsh/gmsh-2.9.1-intel-2015a.eb | 2 ++ 3 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb new file mode 100644 index 0000000000..d971d9f7a0 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb index 1a8738bd04..32895add69 100644 --- a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://geuz.org/getdp/src/'] sources = ['%(name)s-%(version)s-source.tgz'] +builddependencies = [('CMake', '3.2.2')] + dependencies = [ ('GSL', '1.16'), ('PETSc', '3.5.3', versionsuffix), diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb index 00701f2eb2..40e96ab54b 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://geuz.org/gmsh/src/'] sources = ['%(name)s-%(version)s-source.tgz'] +builddependencies = [('CMake', '3.2.2')] + separate_build_dir = True configopts = '-DENABLE_FLTK=0' -- GitLab From fcb028610093a89c404bb865e01557c8bd46243d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 21:03:39 +0200 Subject: [PATCH 256/992] fix getdp easyconfig filename --- ...5.0-intel-2015a.eb => getdp-2.5.0-intel-2015a-Python-2.7.9.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/getdp/{getdp-2.5.0-intel-2015a.eb => getdp-2.5.0-intel-2015a-Python-2.7.9.eb} (100%) diff --git a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb similarity index 100% rename from easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb rename to easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb -- GitLab From 7b6b3008dc49190e0bc2e48f3914661ade0a6448 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 22:05:21 +0200 Subject: [PATCH 257/992] fix sanity check paths for getdp --- .../g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb index 32895add69..bf0165977f 100644 --- a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb @@ -23,4 +23,9 @@ dependencies = [ separate_build_dir = True +sanity_check_paths = { + 'files': ['bin/getdp'], + 'dirs': ['share'], +} + moduleclass = 'math' -- GitLab From 0d53fd727044b2a5de8c7449d51de680e09c6f83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 22:53:55 +0200 Subject: [PATCH 258/992] add working easyconfigs for HPL, zlib, Szip with CrayGNU 5.1.29 toolchain --- .../h/HPL/HPL-2.1-CrayGNU-5.1.29.eb | 18 +++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.1.29.eb | 23 +++++++++++++++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb | 22 ++++++++++++++++++ 3 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..806d976659 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..5a2850640d --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'shared': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..737b571621 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'shared': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From cd71dfbddb7f53bf75478689ebe433bd0236b20e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 23:02:52 +0200 Subject: [PATCH 259/992] add easyconfig for Libint 1.1.4 with CrayGNU 5.1.29 toolchain --- .../l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..7d4d9128c9 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' -- GitLab From 485182e90af909ae96d86bdf5dbfcff5b49c88bb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Apr 2015 16:11:51 +0200 Subject: [PATCH 260/992] specify fftw dep in Cray toolchain easyconfigs as an external dep --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 2 +- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 2 +- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 2 +- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb | 2 +- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb index 45d88cae31..f5df8a066a 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.0')] +dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb index 78c6b82ec4..524d8e18e6 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.2')] +dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index f5228016b8..cf8d95ff05 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.0')] +dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index 0577186f67..b811ad7ed5 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.2')] +dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb index 9f906e92b4..8e4b5fe50e 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.0')] +dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb index bcd630f2e9..b460d5e453 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.2')] +dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] moduleclass = 'toolchain' -- GitLab From 8b46e6671a2b1d719b649e3df568125326d7da7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Apr 2015 19:51:06 +0200 Subject: [PATCH 261/992] {tools}[GCC/4.9.2] parallel 20150322 --- .../p/parallel/parallel-20150322-GCC-4.9.2.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb new file mode 100644 index 0000000000..5819c52290 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20150322' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/parallel'] + +dependencies = [ + ('Perl', '5.20.1', '-bare'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 3430ac8b491a4dbf2cda7bb17f9fe397b8cbbbb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Apr 2015 19:54:02 +0200 Subject: [PATCH 262/992] bump Perl version in parallel dep to latest --- .../p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb | 19 +++++++++++++++++++ .../p/parallel/parallel-20150322-GCC-4.9.2.eb | 2 +- 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb new file mode 100644 index 0000000000..a79c30c3b2 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb @@ -0,0 +1,19 @@ +name = 'Perl' +version = '5.20.2' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +runtest = 'test' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb index 5819c52290..d8b12a2b08 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/parallel'] dependencies = [ - ('Perl', '5.20.1', '-bare'), + ('Perl', '5.20.2', '-bare'), ] sanity_check_paths = { -- GitLab From 2528867b9d244f4bab88d7d73c983e885b4498b8 Mon Sep 17 00:00:00 2001 From: Petar Forai Date: Wed, 22 Apr 2015 01:48:23 +0200 Subject: [PATCH 263/992] Added initial GROMACS 4.6.5 support for CrayGNU. Need to add -mt and -hybrid suffixes. --- .../g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..e8c3fd1883 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.5' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.1.3', '', True)] + +runtest = False + +moduleclass = 'bio' -- GitLab From 29f05410639f3894651b8075469659144a2e6e8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 09:39:33 +0200 Subject: [PATCH 264/992] add easyconfig for GROMACS + ncurses/CMake deps with CrayGNU 5.1.29 --- .../c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb | 23 ++++++++++++ .../GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb | 37 +++++++++++++++++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 22 +++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..68df962efa --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb new file mode 100644 index 0000000000..c7618bc1f3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..64defc00e8 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'shared': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' -- GitLab From 511854dff8266600d50b2d75a13e1ef055197ed4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 09:40:42 +0200 Subject: [PATCH 265/992] remove GROMACS 4.6.5 with CrayGNU --- .../g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb deleted file mode 100644 index e8c3fd1883..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.5' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -builddependencies = [('CMake', '3.1.3', '', True)] - -runtest = False - -moduleclass = 'bio' -- GitLab From 3adbc1318e829bef3ba5a8a2fe40c01deead9fd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 22 Apr 2015 09:47:17 +0200 Subject: [PATCH 266/992] Toolchain intel-2014.06 including HPL-2.1 --- .../h/HPL/HPL-2.1-intel-2014.06.eb | 18 +++++++++++++++ .../i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb | 21 +++++++++++++++++ .../imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb | 22 ++++++++++++++++++ ...4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 19 +++++++++++++++ .../easyconfigs/i/intel/intel-2014.06.eb | 23 +++++++++++++++++++ 5 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2014.06.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb new file mode 100644 index 0000000000..38c3e337e3 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb new file mode 100644 index 0000000000..6927105428 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '5.5.0' +versionsuffix = '-GCC-4.8.3' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '5.192' +compver = '2013.%s' % suff + +dependencies = [ # version/released + ('icc', compver, versionsuffix), # 28 Apr 2014 + ('ifort', compver, versionsuffix), # 28 Apr 2014 + ('impi', '4.1.1.036', '', ('iccifort', '%s%s' % (compver, versionsuffix))), # 06 Mar 2014 +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb new file mode 100644 index 0000000000..e04b151136 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.0.5.192' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '5.5.0-GCC-4.8.3'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +interfaces = True + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb new file mode 100644 index 0000000000..00ee030d34 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '4.1.1.036' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2013.5.192-GCC-4.8.3'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2014.06.eb b/easybuild/easyconfigs/i/intel/intel-2014.06.eb new file mode 100644 index 0000000000..57c2903c57 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2014.06.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'intel' +version = '2014.06' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '5.192' +compver = '2013.%s' % suff + +gccsuff = '-GCC-4.8.3' + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '4.1.1.036', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.0.5.192', '', ('iimpi', '5.5.0%s' % gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From cf377e97fa10de64eb15963e45e25c8ceaae4888 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 12:07:43 +0200 Subject: [PATCH 267/992] include PrgEnv and cray-libsci deps in CrayGNU toolchains --- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 6 +++++- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index cf8d95ff05..9f424cdc02 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -8,6 +8,10 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), + ('cray-libsci/13.0.1', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + ('fftw/3.3.4.0', EXTERNAL_MODULE), +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index b811ad7ed5..37804fbb5c 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -8,6 +8,10 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), + ('cray-libsci/13.0.3', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] moduleclass = 'toolchain' -- GitLab From ba093636f1a248850f323619b8988204dd966172 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 14:14:35 +0200 Subject: [PATCH 268/992] enable pic option in expat easyconfigs --- easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb | 1 + 18 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb index e10b56409e..5ec94cc902 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb index 32e37ffc4e..ff49fa9059 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgmpolf', 'version': '1.1.6'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb index a5482a0de8..e94cc361d0 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgmvolf', 'version': '1.1.12rc1'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb index 77192999ec..faee47738e 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb index 7548d8a264..292f27fff3 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgoolf', 'version': '1.1.7'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb index 35e32ef7da..e68977279b 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb index 1381b2b8cd..600e38e8b5 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb index 1df1944fe7..5bf2380173 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb index 23118879c5..1e273d6bd7 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'gmvolf', 'version': '1.7.12rc1'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb index 207aea5fd5..7fee445ae4 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb index ccfb1c69db..c409db262d 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb index 3d951c24c9..988d22cea6 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb index 6fe54d636d..40d2dd346f 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb index f59fe3f2c0..659d23c4d0 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb index 7717261400..c97465c9f1 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb index 45acf6dd3e..7960b1c2df 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb index f76c746c5e..1c0523995a 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb index 0eb1188648..084ab12246 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -- GitLab From 05e3d12dda5b6d5862b21144d11e0af3ee50bc9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 17:47:55 +0200 Subject: [PATCH 269/992] add easyconfigs for CP2K + deps with CrayGNU/5.1.29 --- .../b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb | 22 +++++++++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb | 38 +++++++++++++++++++ .../f/flex/flex-2.5.39-CrayGNU-5.1.29.eb | 14 +++++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb | 32 ++++++++++++++++ .../m/M4/M4-1.4.17-CrayGNU-5.1.29.eb | 23 +++++++++++ 5 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..96873ab500 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..e1f9bdb729 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..a6d2ced89c --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..548d650cde --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..de4b325756 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From b99801a68b103fa5037f4a15aaad321dd0c2bd0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 17:57:56 +0200 Subject: [PATCH 270/992] fix sources/source_urls in Octave easyconfig --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index 131eedc724..f4320d6460 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -8,8 +8,8 @@ description = """GNU Octave is a high-level interpreted language, primarily inte toolchain = {'name': 'foss', 'version': '2015a'} -sources = [GNU_SOURCE] -source_urls = ['http://ftpmirror.gnu.org/octave/'] +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] configopts = '--with-blas="${LIBBLAS}"' -- GitLab From 4e6b0a299a1645227e03f8f7520846553a1465dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 20:54:44 +0200 Subject: [PATCH 271/992] {math}[intel/2015a] Octave 3.8.2 --- .../o/Octave/Octave-3.8.2-foss-2015a.eb | 4 +-- .../o/Octave/Octave-3.8.2-intel-2015a.eb | 29 +++++++++++++++++ .../o/Octave/Octave-3.8.2_intel.patch | 32 +++++++++++++++++++ 3 files changed, 63 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index f4320d6460..da90d7cb9f 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -11,14 +11,14 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -configopts = '--with-blas="${LIBBLAS}"' - dependencies = [ ('PCRE', '8.36'), ('ncurses', '5.9'), ('libreadline', '6.3'), ] +configopts = '--with-blas="${LIBBLAS}"' + sanity_check_paths = { 'files': ['bin/octave'], 'dirs': [] diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb new file mode 100644 index 0000000000..a7b0eeec4a --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '3.8.2' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['Octave-%(version)s_intel.patch'] + +dependencies = [ + ('PCRE', '8.36'), + ('ncurses', '5.9'), + ('libreadline', '6.3'), +] + +configopts = '--with-blas="${LIBBLAS}"' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch new file mode 100644 index 0000000000..3bc21ba24d --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch @@ -0,0 +1,32 @@ +avoid "declaration is incompatible with previous" style error message +cfr. http://lists.gnu.org/archive/html/help-octave/2011-10/msg00438.html +by Kenneth Hoste (HPC-UGent) +--- octave-3.8.2/libgnu/stdio.in.h.orig 2015-04-22 20:12:39.436847845 +0200 ++++ octave-3.8.2/libgnu/stdio.in.h 2015-04-22 20:15:20.800889451 +0200 +@@ -633,7 +633,7 @@ + _GL_FUNCDECL_RPL (getchar, int, (void)); + _GL_CXXALIAS_RPL (getchar, int, (void)); + # else +-_GL_CXXALIAS_SYS (getchar, int, (void)); ++//_GL_CXXALIAS_SYS (getchar, int, (void)); + # endif + _GL_CXXALIASWARN (getchar); + #endif +@@ -907,7 +907,7 @@ + _GL_FUNCDECL_RPL (putchar, int, (int c)); + _GL_CXXALIAS_RPL (putchar, int, (int c)); + # else +-_GL_CXXALIAS_SYS (putchar, int, (int c)); ++//_GL_CXXALIAS_SYS (putchar, int, (int c)); + # endif + _GL_CXXALIASWARN (putchar); + #endif +@@ -1261,7 +1261,7 @@ + /* Need to cast, because on Solaris, the second parameter is + __va_list args + and GCC's fixincludes did not change this to __gnuc_va_list. */ +-_GL_CXXALIAS_SYS_CAST (vprintf, int, (const char *format, va_list args)); ++//_GL_CXXALIAS_SYS_CAST (vprintf, int, (const char *format, va_list args)); + # endif + _GL_CXXALIASWARN (vprintf); + #endif -- GitLab From 9281c89c26232fbe8b18dcc1d2366de0aaaffd48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 21:34:22 +0200 Subject: [PATCH 272/992] fix patch for building Octave with Intel compilers, add sanity check command --- .../o/Octave/Octave-3.8.2-foss-2015a.eb | 2 + .../o/Octave/Octave-3.8.2-intel-2015a.eb | 2 + .../o/Octave/Octave-3.8.2_intel.patch | 55 +++++++++---------- 3 files changed, 29 insertions(+), 30 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index da90d7cb9f..2bf046bbd9 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -24,4 +24,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = [('octave', '--eval "1+2"')] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb index a7b0eeec4a..a4fb263cdc 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = [('octave', '--eval "1+2"')] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch index 3bc21ba24d..20560be7e6 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch @@ -1,32 +1,27 @@ -avoid "declaration is incompatible with previous" style error message -cfr. http://lists.gnu.org/archive/html/help-octave/2011-10/msg00438.html -by Kenneth Hoste (HPC-UGent) ---- octave-3.8.2/libgnu/stdio.in.h.orig 2015-04-22 20:12:39.436847845 +0200 -+++ octave-3.8.2/libgnu/stdio.in.h 2015-04-22 20:15:20.800889451 +0200 -@@ -633,7 +633,7 @@ - _GL_FUNCDECL_RPL (getchar, int, (void)); - _GL_CXXALIAS_RPL (getchar, int, (void)); - # else --_GL_CXXALIAS_SYS (getchar, int, (void)); -+//_GL_CXXALIAS_SYS (getchar, int, (void)); - # endif - _GL_CXXALIASWARN (getchar); +fix build issue with Intel compilers that manifests itself as: +../../libgnu/stdio.h(948): error: declaration is incompatible with previous "getchar" (declared at line 542 of "/usr/include/stdio.h") + _GL_CXXALIAS_SYS (getchar, int, (void)); + ^ +see http://octave.1599824.n4.nabble.com/Build-issues-with-libgnu-tt4666148.html#a4666416 +patch available via https://savannah.gnu.org/bugs/index.php?43171 +--- octave-3.8.2/libgnu/fcntl.in.h ++++ octave-3.8.2/libgnu//fcntl.in.h +@@ -34,7 +34,7 @@ + extern "C" { ... } block, which leads to errors in C++ mode with the + overridden from gnulib. These errors are known to be gone + with g++ version >= 4.3. */ +-#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))) ++#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && (defined __ICC || !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)))) + # include #endif -@@ -907,7 +907,7 @@ - _GL_FUNCDECL_RPL (putchar, int, (int c)); - _GL_CXXALIAS_RPL (putchar, int, (int c)); - # else --_GL_CXXALIAS_SYS (putchar, int, (int c)); -+//_GL_CXXALIAS_SYS (putchar, int, (int c)); - # endif - _GL_CXXALIASWARN (putchar); - #endif -@@ -1261,7 +1261,7 @@ - /* Need to cast, because on Solaris, the second parameter is - __va_list args - and GCC's fixincludes did not change this to __gnuc_va_list. */ --_GL_CXXALIAS_SYS_CAST (vprintf, int, (const char *format, va_list args)); -+//_GL_CXXALIAS_SYS_CAST (vprintf, int, (const char *format, va_list args)); - # endif - _GL_CXXALIASWARN (vprintf); + #@INCLUDE_NEXT@ @NEXT_FCNTL_H@ +@@ -53,7 +53,7 @@ + extern "C" { ... } block, which leads to errors in C++ mode with the + overridden from gnulib. These errors are known to be gone + with g++ version >= 4.3. */ +-#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))) ++#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && (defined __ICC || !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)))) + # include #endif + /* The include_next requires a split double-inclusion guard. */ + -- GitLab From 5e877df0dacccfa40d615e938848de522483e927 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 21:48:53 +0200 Subject: [PATCH 273/992] complete patch for building Octave with Intel --- .../o/Octave/Octave-3.8.2_intel.patch | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch index 20560be7e6..ec623d4749 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch @@ -25,3 +25,27 @@ patch available via https://savannah.gnu.org/bugs/index.php?43171 #endif /* The include_next requires a split double-inclusion guard. */ +--- octave-3.8.2/liboctave/cruft/misc/quit.h.orig 2015-04-22 21:47:08.614133593 +0200 ++++ octave-3.8.2/liboctave/cruft/misc/quit.h 2015-04-22 21:47:24.584562436 +0200 +@@ -23,16 +23,16 @@ + #if !defined (octave_quit_h) + #define octave_quit_h 1 + +-#ifdef __cplusplus +-#include +-extern "C" { +-#endif +- + #include + + #include + #include + ++#ifdef __cplusplus ++#include ++extern "C" { ++#endif ++ + #if defined (__WIN32__) && ! defined (_POSIX_VERSION) + + #define WIN32_LEAN_AND_MEAN -- GitLab From 3ad51d6e3c3eb177dd97e9f202bd822bc63907ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 22:26:02 +0200 Subject: [PATCH 274/992] add easyconfigs for Python/numpy/scipy with CrayGNU 5.1.29 --- ...numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.1.29-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 107 ++++++++++++++++++ ...cipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb | 19 ++++ 4 files changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb new file mode 100644 index 0000000000..49b27458ee --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb new file mode 100644 index 0000000000..2ec3cb1dc8 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..4ef1c682d1 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb new file mode 100644 index 0000000000..d6c03f828c --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' -- GitLab From fd0f971d2ce6b217255a2a757d738f18d6e50cda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 23:29:04 +0200 Subject: [PATCH 275/992] add missing bzip2 easyconfig with CrayGNU 5.1.29 --- .../b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..a04591dede --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' -- GitLab From c0f36ba76e8fce6cb7239b7dc0b2aa7f280c5cd9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 23:29:41 +0200 Subject: [PATCH 276/992] add missing libreadline easyconfig with CrayGNU 5.1.29 --- .../libreadline-6.3-CrayGNU-5.1.29.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..8b8b71eae5 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' -- GitLab From 2d387c0a2898473c987ad093100f56dcdf4c36a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Thu, 23 Apr 2015 09:37:26 +0200 Subject: [PATCH 277/992] OpenCV-2.4.9-intel-2014.06 anddependencies --- .../a/ant/ant-1.9.3-Java-1.7.0_79.eb | 26 +++++ .../b/bzip2/bzip2-1.0.6-intel-2014.06.eb | 15 +++ .../c/CMake/CMake-3.0.0-intel-2014.06.eb | 22 +++++ .../f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb | 28 ++++++ .../g/GLib/GLib-2.40.0-intel-2014.06.eb | 21 +++++ .../g/gettext/gettext-0.19.2-intel-2014.06.eb | 18 ++++ .../j/JUnit/JUnit-4.11-Java-1.7.0_79.eb | 25 +++++ .../j/JasPer/JasPer-1.900.1-intel-2014.06.eb | 21 +++++ easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb | 15 +++ .../l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb | 19 ++++ .../l/libffi/libffi-3.1-intel-2014.06.eb | 23 +++++ .../libjpeg-turbo-1.3.1-intel-2014.06.eb | 24 +++++ .../l/libpng/libpng-1.6.12-intel-2014.06.eb | 19 ++++ .../libreadline-6.3-intel-2014.06.eb | 27 ++++++ .../n/NASM/NASM-2.11.05-intel-2014.06.eb | 19 ++++ .../n/ncurses/ncurses-5.9-intel-2014.06.eb | 15 +++ .../o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 76 +++++++++++++++ .../p/Python/Python-2.7.8-intel-2014.06.eb | 94 +++++++++++++++++++ .../z/zlib/zlib-1.2.8-intel-2014.06.eb | 24 +++++ 19 files changed, 531 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb new file mode 100644 index 0000000000..e1662e8bf2 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb @@ -0,0 +1,26 @@ +name = 'ant' +version = '1.9.3' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +java = 'Java' +javaver = '1.7.0_79' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +builddependencies = [('JUnit', '4.11', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb new file mode 100644 index 0000000000..567328a2d6 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb new file mode 100644 index 0000000000..447079089d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb new file mode 100644 index 0000000000..36569d20af --- /dev/null +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ffmpeg' +version = '2.4' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX"' + +dependencies = [ + ('NASM', '2.11.05'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb new file mode 100644 index 0000000000..0b2f10e82d --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.40.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.1'), + ('gettext', '0.19.2'), +] +builddependencies = [('Python', '2.7.8')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb new file mode 100644 index 0000000000..238843b206 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.2' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb new file mode 100644 index 0000000000..4c4751893b --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb @@ -0,0 +1,25 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.11' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +java = 'Java' +javaver = '1.7.0_79' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.eb new file mode 100644 index 0000000000..41dba8410e --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb new file mode 100644 index 0000000000..d7b280abb2 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.7.0_79' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb new file mode 100644 index 0000000000..987c5b0636 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.3' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb new file mode 100644 index 0000000000..1db00ffb5e --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libffi.%s' % SHLIB_EXT, 'lib/libffi.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb new file mode 100644 index 0000000000..c76e470179 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.3.1' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb new file mode 100644 index 0000000000..e5160148db --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.12' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb new file mode 100644 index 0000000000..7154c323ba --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb new file mode 100644 index 0000000000..2a7e58d385 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.05' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb new file mode 100644 index 0000000000..e1045e7b9f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb @@ -0,0 +1,15 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb new file mode 100644 index 0000000000..9bed0737f0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -0,0 +1,76 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '2.4.9' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'opt': True, 'optarch': True} + +sources = [SOURCELOWER_ZIP] +source_urls = [('http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/%(version)s', 'download')] + +patches = ['OpenCV-%(version)s_with_IPP.patch'] + +osdependencies = ['gtk2-devel'] + +builddependencies = [ + ('CMake', '3.0.0'), +] + +python = 'Python' +pythonver = '2.7.8' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +java = 'Java' +javaver = '1.7.0_79' + +dependencies = [ + (python, pythonver), + ('zlib', '1.2.8'), + ('ffmpeg', '2.4'), + ('libjpeg-turbo', '1.3.1'), + ('libpng', '1.6.12'), + ('LibTIFF', '4.0.3'), + ('JasPer', '1.900.1'), + (java, javaver ,'', True), + ('ant', '1.9.3', '-%s-%s' % (java,javaver), True), + ('GLib', '2.40.0') +] + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%s/site-packages ' % pythonshortver +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.so ' +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so ' +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.so ' +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.so'] + + [ 'bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade'] ], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver, + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb new file mode 100644 index 0000000000..db0f00951f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -0,0 +1,94 @@ +name = 'Python' +version = '2.7.8' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.1' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-2.7_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +] + +# order is important! +# Version updated 08/JULY/2014 +exts_list = [ + ('setuptools', '5.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.3', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s-mkl.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb new file mode 100644 index 0000000000..7873060724 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +preconfigopts = 'LDSHARED="$CC -shared"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 495f273d92617554442f773a673707cfeaea0403 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 09:52:44 +0200 Subject: [PATCH 278/992] Updated checksum --- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 7a65f31c78..85c24b1b81 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -29,7 +29,7 @@ sources = [ patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] checksums = [ - '37cdc2eb0adf92e421c0841748ac1471', # gcc-5.1.0.tar.bz2 + 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz -- GitLab From 3a22caad5a4aafd57c8db00ad2d88d20c9bcbf30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2015 09:54:21 +0200 Subject: [PATCH 279/992] sync with easyconfigs in develop where needed --- .../l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb | 16 +++++++++++++++- .../l/libffi/libffi-3.1-intel-2014.06.eb | 2 +- .../n/NASM/NASM-2.11.05-intel-2014.06.eb | 11 +++++++++++ .../p/Python/Python-2.7.8-intel-2014.06.eb | 13 ++++++++++--- .../z/zlib/zlib-1.2.8-intel-2014.06.eb | 2 -- 5 files changed, 37 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb index 987c5b0636..e29ed51d54 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb @@ -1,3 +1,14 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## easyblock = 'ConfigureMake' name = 'LibTIFF' @@ -6,7 +17,10 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] toolchain = {'name': 'intel', 'version': '2014.06'} diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb index 1db00ffb5e..4f8e9bd62b 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb @@ -16,7 +16,7 @@ source_urls = [ sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['lib/libffi.%s' % SHLIB_EXT, 'lib/libffi.a'], + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], 'dirs': [], } diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb index 2a7e58d385..8eacf467e7 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb @@ -1,3 +1,14 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## easyblock = 'ConfigureMake' name = 'NASM' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index db0f00951f..54d5edce60 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -22,8 +22,11 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + # order is important! # Version updated 08/JULY/2014 exts_list = [ @@ -49,7 +52,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['https://mpi4py.googlecode.com/files/'], + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], @@ -63,6 +66,9 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -81,6 +87,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), @@ -89,6 +98,4 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb index 7873060724..24f9e69fb8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From 9f8ec0262d4e374fa6a57f40dc8b9b6b68d1c1a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2015 10:13:52 +0200 Subject: [PATCH 280/992] style fix in Octave easyconfigs --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index 2bf046bbd9..eeea60d967 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -17,7 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ] -configopts = '--with-blas="${LIBBLAS}"' +configopts = '--with-blas="$LIBBLAS"' sanity_check_paths = { 'files': ['bin/octave'], diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb index a4fb263cdc..2b1159f006 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [ ('libreadline', '6.3'), ] -configopts = '--with-blas="${LIBBLAS}"' +configopts = '--with-blas="$LIBBLAS"' sanity_check_paths = { 'files': ['bin/octave'], -- GitLab From c3296f64fab24fd62f35f533e1814ba9afa8d359 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 13:27:45 +0200 Subject: [PATCH 281/992] Update GCC easyconfig --- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 85c24b1b81..8a37c34c77 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -23,7 +23,6 @@ sources = [ 'gmp-6.0.0a.tar.bz2', 'mpfr-%s.tar.gz' % mpfr_version, 'mpc-1.0.3.tar.gz', - 'isl-0.14.tar.bz2', ] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] @@ -33,14 +32,11 @@ checksums = [ 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch ] languages = ['c', 'c++', 'fortran'] -#withisl = True - # building GCC sometimes fails if make parallelism is too high, so let's limit it maxparallel = 4 -- GitLab From 90f959d537610594d36dd1f3bd37cfdd044f32f2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 13:27:56 +0200 Subject: [PATCH 282/992] Add GCC with ISL and 3 stage build --- easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb | 53 ++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb new file mode 100644 index 0000000000..49c83175bd --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb @@ -0,0 +1,53 @@ +name = "GCC" +version = '5.1.0' +versionsuffix = 'ISL' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +sanity_check_paths = { + 'files': ['bin/gcc'], + 'dirs': ["."] +} + +moduleclass = 'compiler' -- GitLab From fa38bc69b483bcff92c4d4882700de0954f8cc56 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 13:35:19 +0200 Subject: [PATCH 283/992] Updated version suffix --- easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb index 49c83175bd..acd0ece277 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb @@ -1,6 +1,6 @@ name = "GCC" version = '5.1.0' -versionsuffix = 'ISL' +versionsuffix = '-ISL' homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, -- GitLab From 981ae913f660d72ed08edb7589eb97273a5117ee Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 16:06:02 +0200 Subject: [PATCH 284/992] Only build a ISL enabled version of GCC --- easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb | 53 -------------------- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 4 ++ 2 files changed, 4 insertions(+), 53 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb deleted file mode 100644 index acd0ece277..0000000000 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb +++ /dev/null @@ -1,53 +0,0 @@ -name = "GCC" -version = '5.1.0' -versionsuffix = '-ISL' - -homepage = 'http://gcc.gnu.org/' -description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, - as well as libraries for these languages (libstdc++, libgcj,...).""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -mpfr_version = '3.1.2' - -source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR - 'http://www.multiprecision.org/mpc/download', # MPC official - 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies -] - -sources = [ - SOURCELOWER_TAR_BZ2, - 'gmp-6.0.0a.tar.bz2', - 'mpfr-%s.tar.gz' % mpfr_version, - 'mpc-1.0.3.tar.gz', - 'isl-0.14.tar.bz2', -] - -patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] - -checksums = [ - 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 - 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 - '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz - 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 - '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch -] - -languages = ['c', 'c++', 'fortran'] - -withisl = True - -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - -sanity_check_paths = { - 'files': ['bin/gcc'], - 'dirs': ["."] -} - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 8a37c34c77..4968008ae8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -23,6 +23,7 @@ sources = [ 'gmp-6.0.0a.tar.bz2', 'mpfr-%s.tar.gz' % mpfr_version, 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', ] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] @@ -32,11 +33,14 @@ checksums = [ 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch ] languages = ['c', 'c++', 'fortran'] +withisl = True + # building GCC sometimes fails if make parallelism is too high, so let's limit it maxparallel = 4 -- GitLab From c83c8a1aa6eecac035536643e20914e3c85314b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2015 10:33:53 +0200 Subject: [PATCH 285/992] load cray-libsci versionless --- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 3 ++- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index 9f424cdc02..b105aa0520 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -10,7 +10,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), - ('cray-libsci/13.0.1', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + # cray-libsci is intentionally loaded with specifying a version, loaded by PrgEnv-gnu (version is site-specific) + ('cray-libsci', EXTERNAL_MODULE), ('fftw/3.3.4.0', EXTERNAL_MODULE), ] diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index 37804fbb5c..05afff31a0 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -10,7 +10,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), - ('cray-libsci/13.0.3', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + # cray-libsci is intentionally loaded with specifying a version, loaded by PrgEnv-gnu (version is site-specific) + ('cray-libsci', EXTERNAL_MODULE), # loaded by PrgEnv-gnu ('fftw/3.3.4.2', EXTERNAL_MODULE), ] -- GitLab From a49ebcb5cb34aa948f311f2b7801ce63f762dd8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2015 15:41:02 +0200 Subject: [PATCH 286/992] bump to latest versions (IPython 3.1.0), add Pygments dep for IPython --- ...IPython-3.1.0-intel-2015a-Python-2.7.9.eb} | 7 ++-- ...Q-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb} | 4 +-- ...Q-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb | 31 ------------------ ...Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 30 +++++++++++++++++ ...pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb | 32 +++++++++++++++++++ ...equests-2.6.2-intel-2015a-Python-2.7.9.eb} | 6 ++-- .../util-linux-2.22.2-intel-2015a.eb | 29 ----------------- ...l-2015a.eb => ZeroMQ-3.2.5-intel-2015a.eb} | 6 ++-- 8 files changed, 74 insertions(+), 71 deletions(-) rename easybuild/easyconfigs/i/IPython/{IPython-3.0.0-intel-2015a-Python-2.7.9.eb => IPython-3.1.0-intel-2015a-Python-2.7.9.eb} (88%) rename easybuild/easyconfigs/p/PyZMQ/{PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb => PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb} (94%) delete mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb rename easybuild/easyconfigs/r/requests/{requests-2.6.0-intel-2015a-Python-2.7.9.eb => requests-2.6.2-intel-2015a-Python-2.7.9.eb} (80%) delete mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb rename easybuild/easyconfigs/z/ZeroMQ/{ZeroMQ-3.2.2-intel-2015a.eb => ZeroMQ-3.2.5-intel-2015a.eb} (93%) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb similarity index 88% rename from easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb index bda10584b8..377e678904 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = "PythonPackage" name = 'IPython' -version = '3.0.0' +version = '3.1.0' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -24,8 +24,9 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), ('pysqlite', '2.6.3', versionsuffix), - ('PyZMQ', '14.5.0', '%s-zmq3' % versionsuffix), - ('requests', '2.6.0', versionsuffix) + ('PyZMQ', '14.6.0', '%s-zmq3' % versionsuffix), + ('requests', '2.6.2', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), ] # override extensions sanity check, default filter that imports a Python module doesn't work here diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb similarity index 94% rename from easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb rename to easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb index b297340fc3..182cf6eed5 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'PyZMQ' -version = '14.5.0' +version = '14.6.0' homepage = 'http://www.zeromq.org/bindings:python' description = """Python bindings for ZeroMQ""" @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.9' pythonshortversion = ".".join(pythonversion.split(".")[0:2]) -zmqversion = '3.2.2' +zmqversion = '3.2.5' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb deleted file mode 100644 index 022cf3fe3b..0000000000 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'PyZMQ' -version = '2.2.0.1' - -homepage = 'http://www.zeromq.org/bindings:python' -description = """Python bindings for ZeroMQ""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -python = 'Python' -pythonversion = '2.7.9' -pythonshortversion = ".".join(pythonversion.split(".")[0:2]) -zmqversion = '3.2.2' - -versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) - -dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), -] - -options = {'modulename': 'zmq'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..c6557db043 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.0.2' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..cbbee774d8 --- /dev/null +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'pysqlite' +version = '2.6.3' + +homepage = 'https://pypi.python.org/pypi/pysqlite' +description = """pysqlite is an interface to the SQLite 3.x embedded relational database engine. + It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SQLite', '3.8.8.1'), # also dependency for Python itself +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +options = {'modulename': '%(name)s%(version_major)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb similarity index 80% rename from easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb index 4a577a2051..c746104f6f 100644 --- a/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'requests' -version = '2.6.0' +version = '2.6.2' homepage = 'https://pypi.python.org/pypi/requests/2.6.0' description = """Python http for humans""" @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.9' -pythonshortversion = ".".join(pythonversion.split(".")[0:2]) +pyshortver = ".".join(pythonversion.split(".")[0:2]) versionsuffix = '-%s-%s' % (python, pythonversion) @@ -23,7 +23,7 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pythonshortversion, version, pythonshortversion) ], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb deleted file mode 100644 index 7cdce40ba2..0000000000 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'util-linux' -version = '2.22.2' - -homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' -description = """Set of Linux utilities""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] -sources = [SOURCELOWER_TAR_GZ] - -# disable account related utilities (they need OS dependant pam-devel files) -# disable wall and friends (requires group changing permissions for install user) -# install systemd service files in install dir -configopts = '--disable-chfn-chsh --disable-login --disable-su ' -configopts += '--disable-wall --disable-use-tty-group ' -configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' -configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], - 'dirs': ['include', 'bin', 'share', 'sbin'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-intel-2015a.eb similarity index 93% rename from easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb rename to easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-intel-2015a.eb index 537584a82a..19243eab21 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-intel-2015a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'ZeroMQ' -version = '3.2.2' +version = '3.2.5' homepage = 'http://www.zeromq.org/' description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. @@ -16,7 +16,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://download.zeromq.org/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['ZeroMQ-%(version)s_icc.patch'] +patches = ['ZeroMQ-3.2.2_icc.patch'] # --with-pgm will use shipped OpenPGM (in foreign subdir) configopts = '--with-pic --with-system-pgm ' @@ -25,7 +25,7 @@ configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ ('OpenPGM', '5.2.122'), - ('util-linux', '2.22.2'), + ('util-linux', '2.26.1'), ] sanity_check_paths = { -- GitLab From 77d9f566d3b11b2445277589eba80aacf845a598 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2015 15:46:50 +0200 Subject: [PATCH 287/992] minor style fixes --- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb | 4 ++-- .../p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb | 5 ++--- .../p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 3 +-- .../r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb | 3 +-- 4 files changed, 6 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb index 9ac5fd9480..bb2adb94d7 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb @@ -12,8 +12,8 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://%s.googlecode.com/files/' % (name.lower())] -sources = ['%s-%s.tar.gz' % ('libpgm', version)] +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb index 182cf6eed5..e38ac2e143 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.9' -pythonshortversion = ".".join(pythonversion.split(".")[0:2]) +pyshortver = '.'.join(pythonversion.split('.')[:2]) zmqversion = '3.2.5' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) @@ -27,8 +27,7 @@ options = {'modulename': 'zmq'} sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], } moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb index c6557db043..06251d7872 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonversion = '2.7.9' -pyshortver = ".".join(pythonversion.split(".")[0:2]) +pyshortver = '.'.join(pythonversion.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonversion) @@ -27,4 +27,3 @@ sanity_check_paths = { } moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb index c746104f6f..c8c3ba9720 100644 --- a/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.9' -pyshortver = ".".join(pythonversion.split(".")[0:2]) +pyshortver = '.'.join(pythonversion.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonversion) @@ -27,4 +27,3 @@ sanity_check_paths = { } moduleclass = 'devel' - -- GitLab From dac9ed1317d25a0ef9bb73f54dcd6d23357698d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Apr 2015 01:38:53 +0200 Subject: [PATCH 288/992] don't include cray-libsci as direct toolchain component --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 5 ++++- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 5 ++++- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 4 +--- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 4 +--- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb | 5 ++++- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb | 5 ++++- 6 files changed, 18 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb index f5df8a066a..766d96d756 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -8,6 +8,9 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.0', EXTERNAL_MODULE), +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb index 524d8e18e6..7a2e621e24 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -8,6 +8,9 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index b105aa0520..b3e7499933 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -9,9 +9,7 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), - # cray-libsci is intentionally loaded with specifying a version, loaded by PrgEnv-gnu (version is site-specific) - ('cray-libsci', EXTERNAL_MODULE), + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci ('fftw/3.3.4.0', EXTERNAL_MODULE), ] diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index 05afff31a0..4015746894 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -9,9 +9,7 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), - # cray-libsci is intentionally loaded with specifying a version, loaded by PrgEnv-gnu (version is site-specific) - ('cray-libsci', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci ('fftw/3.3.4.2', EXTERNAL_MODULE), ] diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb index 8e4b5fe50e..7c17b80f7e 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -8,6 +8,9 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.0', EXTERNAL_MODULE), +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb index b460d5e453..edaac85f54 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -8,6 +8,9 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] moduleclass = 'toolchain' -- GitLab From 0ec82f30b35190fcb0b0c6044892a96c7a9b5865 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Apr 2015 14:21:29 +0200 Subject: [PATCH 289/992] add HPL easyconfigs using Cray toolchains --- .../h/HPL/HPL-2.1-CrayCCE-5.1.29.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayCCE-5.2.25.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayGNU-5.1.29.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayGNU-5.2.25.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-5.1.29.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-5.2.25.eb | 18 +++++++++++++++ .../easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch | 11 ++++++++++ 7 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb new file mode 100644 index 0000000000..a7abc8534e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '5.1.29'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb new file mode 100644 index 0000000000..109c7ddafc --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..806d976659 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..b4acf0c1bc --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb new file mode 100644 index 0000000000..c8cac688c8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '5.1.29'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb new file mode 100644 index 0000000000..0344d227a5 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '5.2.25'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch new file mode 100644 index 0000000000..d0e0a51bc5 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch @@ -0,0 +1,11 @@ +--- hpl-2.1/makes/Make.ptest.orig 2015-04-25 13:46:18.668624435 +0200 ++++ hpl-2.1/makes/Make.ptest 2015-04-25 13:47:20.958060830 +0200 +@@ -73,7 +73,7 @@ + ( $(CP) ../HPL.dat $(BINdir) ) + # + dexe.grd: $(HPL_pteobj) $(HPLlib) +- $(LINKER) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) ++ LINKER=`which ld` $(CC) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) + $(MAKE) $(BINdir)/HPL.dat + $(TOUCH) dexe.grd + # -- GitLab From e902fa555ec2d11b51bd154740345d2087ea36bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Apr 2015 14:29:08 +0200 Subject: [PATCH 290/992] fix HPL patch + add description --- easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch index d0e0a51bc5..799444d4e2 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch @@ -1,3 +1,5 @@ +Cray compiler don't like having $LINKER set to a non-absolute path +author: Kenneth Hoste (HPC-UGent) --- hpl-2.1/makes/Make.ptest.orig 2015-04-25 13:46:18.668624435 +0200 +++ hpl-2.1/makes/Make.ptest 2015-04-25 13:47:20.958060830 +0200 @@ -73,7 +73,7 @@ @@ -5,7 +7,7 @@ # dexe.grd: $(HPL_pteobj) $(HPLlib) - $(LINKER) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) -+ LINKER=`which ld` $(CC) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) ++ LINKER=`which ld` $(LINKER) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) $(MAKE) $(BINdir)/HPL.dat $(TOUCH) dexe.grd # -- GitLab From 77df251fcd68b611bb4e93f021d1452ce83de448 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 16:19:35 +0200 Subject: [PATCH 291/992] use proper Bundle easyblock for biodeps/PRACE --- .../easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb | 2 +- easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb | 2 +- easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb index 0a0256d97d..428ecbe9cf 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb index d8d026cace..6fcc534d72 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb index 878f45a16d..34a00add44 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb index 63eda1f427..1091497ff7 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb index 061dd6e110..849c3d613e 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/ ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'PRACE' version = '20130605' diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb index 84d13bb360..63cc6c8164 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/ ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'PRACE' version = '20130605' -- GitLab From 7cce6b48a59220705d011495b069f79d1d6f35c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 16:25:05 +0200 Subject: [PATCH 292/992] bump version to 2.1.0 and update release notes --- RELEASE_NOTES | 39 ++++++++++++++++++++++++++++++++++++--- setup.py | 4 ++-- 2 files changed, 38 insertions(+), 5 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b504cb01ce..b83a7af107 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,16 +3,49 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,344 easyconfig files, for 581 different software packages, -32 different (compiler) toolchains and 6 software bundles. +The latest version of easybuild-easyconfig provides 3,344 easyconfig files, for 608 different software packages, +33 different (compiler) toolchains and 8 software bundles. +v2.1.0 (April 28th 2015) +------------------------ + +- added example easyconfig files for 27 new software packages: + AFNI (#1322, #1521), BCFtools (#1492), getdp (#1518), gmsh (#1518), gtest (#1244), hanythingondemand (#1530), + mawk (#1369), Minimac (#815), Minimac3 (#1502), monty (#1548), Octave (#1563), pbs_python (#1530), pigz (#1036), + Pygments (#1536), pyhull (#1539), pymatgen (#1549), PyQt (#1322, #1521), Ray (#1494), requests (#1536), + seqtk (#1524), SIP (#1322, #1521), S-Lang (#1369), Spark (#1554), spglib (#1549), TINKER (#1465), tmux (#1369), + Xmipp (#1489) +- added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE + - initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558) +- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3, PETSc/SLEPc v3.5.3, WIEN2k v14.1 +- various other enhancements, including: + - include 'pbr' dependency for 'lockfile' Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (#1462, #1540) + - include SQLite as dependency in Python v2.7.9 easyconfigs (#1468) + - set $LD_PRELOAD for Hoard and jemalloc (#1470) + - fix homepage in SCOTCH easyconfigs (#1485) + - adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510) + - enable pic option in expat easyconfigs (#1562) +- various bug fixes, including: + - adding missing zlib dependency in all Tcl easyconfig files (#1344) + - fix homepage in FLUENT easyconfigs (#1472) + - use --with-verbs rather than deprecated --with-openib in OpenMPI configure options (#1511) + - stop relying on OS_NAME constant to specify OS dependencies in OpenMPI easyconfigs (#1512) + - replace use of $root with %(installdir)s to ensure compatibility with module files in Lua syntax (#1532) + - stop relying on $MKLROOT in ROOT easyconfigs (#1537) + - use proper Bundle easyblock for biodeps/PRACE (#1566) v2.0.0 (March 6th 2015) ----------------------- feature + bugfix release - added example easyconfig files for 29 new software packages: - bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568), fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389), jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242), rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), ZPAQ (#1242) + bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568), + fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389), + jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242), + rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), + ZPAQ (#1242) - added easyconfigs for new (common) toolchains foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) - added new software bundle: Autotools (#1385) diff --git a/setup.py b/setup.py index e23ed2d782..5b55ee3e55 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2013 Ghent University +# Copyright 2012-2015 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = "2.1.0dev" +VERSION = '2.1.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 91460c6b94ed03715d96d93760f19ee04974fcca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 16:52:27 +0200 Subject: [PATCH 293/992] add easyconfig for WRF + deps with CrayGNU --- .../j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb | 21 ++++++++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb | 39 ++++++++++++++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 41 +++++++++++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..feca7c584a --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..6245093966 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'shared': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb new file mode 100644 index 0000000000..3806e63de1 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' -- GitLab From b8d75d3267feaad5e1e28db4577e8f1d383b3be1 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sun, 26 Apr 2015 17:18:16 +0200 Subject: [PATCH 294/992] added http://www.bioconductor.org/packages/release/bioc/src/contrib/ as download url for bioconductor packages --- easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 1 + easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb | 1 + 17 files changed, 45 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb index 8468c6029d..d91d0ca1fd 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb index 84d3f3e99e..517c6d157a 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb index 70126d1ce6..b2152142eb 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb index 3a90cc17eb..9414cfc682 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb index 201aa6b636..4b3f70cab0 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb index 65f22fa5a8..4434fbdf2a 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb index 2672165c50..174451bf44 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb index 2f2b2a553e..cc29570d01 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb index 2d510cfe36..4b201ba947 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb index 3bc73c713b..5280f5e5c7 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb index 580cc3effd..8fababc358 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb index 1bda6f96bc..549134c6cc 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb index ba677bcf6d..e7c9c708cc 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb @@ -31,7 +31,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb b/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb index 37633fc50a..91ba061891 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb @@ -32,7 +32,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index e60a4bb6fd..d92fd5ff79 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -34,6 +34,7 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb index a73e438a8c..d111c454b9 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb @@ -34,6 +34,7 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb index 99a39db56a..a5cec405ac 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb @@ -34,6 +34,7 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', -- GitLab From 87026420edafa0ed4ca97bfc48ff6d1700adca52 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sun, 26 Apr 2015 17:23:49 +0200 Subject: [PATCH 295/992] updated urls for data and experiments data --- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 2 ++ easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb | 2 ++ easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index d92fd5ff79..bcd67f42d0 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -35,6 +35,8 @@ ext_options = { bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb index d111c454b9..467f0009f8 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb @@ -35,6 +35,8 @@ ext_options = { bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb index a5cec405ac..813bbd8f5d 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb @@ -35,6 +35,8 @@ ext_options = { bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', -- GitLab From 0c375816933c4bc1edb21de240aff26d2fb6a7e4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sun, 26 Apr 2015 17:33:48 +0200 Subject: [PATCH 296/992] added 3.1.3 easyconfigs --- .../easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 384 ++++++++++++++++++ .../easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 383 +++++++++++++++++ 2 files changed, 767 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb new file mode 100644 index 0000000000..ad11c875f8 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -0,0 +1,384 @@ +name = 'R' +version = '3.1.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.7.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.14', ext_options), + ('formatR', '1.0', ext_options), + ('gtools', '3.4.1', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.4', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.2', ext_options), + ('markdown', '0.7.4', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-6', ext_options), + ('mclust', '4.4', ext_options), + ('RANN', '2.4.1', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.6-6', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-16', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.6-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.55.0-3', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.7', ext_options), + ('longitudinal', '1.1.11', ext_options), + ('checkmate', '1.5.2', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.11.3', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-9', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-4', ext_options), + ('stringr', '0.6.2', ext_options), + ('evaluate', '0.5.5', ext_options), + ('logspline', '2.1.5', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-3', 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('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-63', ext_options), + ('survival', '2.38-1', ext_options), + ('gam', '1.09.1', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-14', ext_options), + ('zoo', '1.7-12', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.22-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('lmtest', '0.9-33', ext_options), + ('mnormt', '1.5-1', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2012.9-1', ext_options), + ('lava', '1.4.0', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.8', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-2', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-9', ext_options), + ('VGAM', '0.9-7', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.11', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.1.33', ext_options), + ('R.utils', '2.0.0', ext_options), + ('R.matlab', '3.2.0', ext_options), + ('BiocGenerics', '0.12.1', bioconductor_options), + ('Biobase', '2.26.0', bioconductor_options), + ('S4Vectors', '0.4.0', bioconductor_options), + ('IRanges', '2.0.1', bioconductor_options), + ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('AnnotationDbi', '1.28.2', bioconductor_options), + ('XVector', '0.6.0', bioconductor_options), + ('zlibbioc', '1.12.0', bioconductor_options), + ('Biostrings', '2.34.1', bioconductor_options), + ('GenomicRanges', '1.18.4', bioconductor_options), + ('Rsamtools', '1.18.3', bioconductor_options), + ('BiocParallel', '1.0.3', bioconductor_options), + ('GenomicAlignments', '1.2.2', bioconductor_options), + ('ShortRead', '1.24.0', bioconductor_options), + ('graph', '1.44.1', bioconductor_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-0', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('gtable', '0.1.2', ext_options), + ('reshape2', '1.4.1', ext_options), + ('proto', '0.3-10', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.2.4', ext_options), + ('ggplot2', '1.0.1', ext_options), + ('Hmisc', '3.15-0', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-45', ext_options), + ('data.table', '1.9.4', ext_options), + ('igraph', '0.7.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.2', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.16.0', ext_options), + ('ROCR', '1.0-5', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.0.1', ext_options), + ('shiny', '0.11.1', ext_options), + ('adegenet', '1.4-2', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.3-33', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '1.9-8', ext_options), + ('labdsv', '1.6-1', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('polspline', '1.1.9', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('rms', '4.3-0', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('knitr', '1.9', ext_options), + ('statmod', '1.4.20', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('affyio', '1.34.0', bioconductor_options), + ('BiocInstaller', '1.16.2', bioconductor_options), + ('preprocessCore', '1.28.0', bioconductor_options), + ('affy', '1.44.0', bioconductor_options), + ('GO.db', '3.0.0', bioconductor_options), + ('limma', '3.22.7', bioconductor_options), + ('RBGL', '1.42.0', bioconductor_options), + ('org.Hs.eg.db', '3.0.0', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), + ('KEGG.db', '3.0.0', bioconductor_options), + ('annaffy', '1.38.0', bioconductor_options), + ('gcrma', '2.38.0', bioconductor_options), + ('oligoClasses', '1.28.0', bioconductor_options), + ('edgeR', '3.8.6', bioconductor_options), + ('PFAM.db', '3.0.0', bioconductor_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('baySeq', '2.0.50', bioconductor_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('qvalue', '1.43.0', bioconductor_options), + ('impute', '1.40.0', bioconductor_options), + ('matrixStats', '0.14.0', ext_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.20.0', bioconductor_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.29', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-6', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('hgu133plus2.db', '3.0.0', bioconductor_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.14', ext_options), + ('kohonen', '2.0.15', ext_options), + ('base64', '1.1', ext_options), + ('illuminaio', '0.8.0', bioconductor_options), + ('registry', '0.2', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('bumphunter', '1.6.0', bioconductor_options), + ('multtest', '2.22.0', bioconductor_options), + ('siggenes', '1.40.0', bioconductor_options), + ('nleqslv', '2.6', ext_options), + ('DynDoc', '1.44.0', bioconductor_options), + ('genoset', '1.20.0', bioconductor_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.2', ext_options), + ('multtest', '2.22.0', bioconductor_options), + ('NOISeq', '2.8.0', bioconductor_options), + ('openxlsx', '2.4.0', ext_options), + ('Rgraphviz', '2.10.0', bioconductor_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('reshape', '0.8.5', ext_options), + ('RNASeqPower', '1.6.0', bioconductor_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('Rsubread', '1.16.1', bioconductor_options), +] + +moduleclass = 'lang' -- GitLab From 4c44a3dead34859d7935cd66ca44050fa455cf1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 20:26:47 +0200 Subject: [PATCH 297/992] include PR #1568 --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b83a7af107..2282d108e0 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -27,6 +27,7 @@ v2.1.0 (April 28th 2015) - fix homepage in SCOTCH easyconfigs (#1485) - adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510) - enable pic option in expat easyconfigs (#1562) + - extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (#1568) - various bug fixes, including: - adding missing zlib dependency in all Tcl easyconfig files (#1344) - fix homepage in FLUENT easyconfigs (#1472) -- GitLab From 17301a204cb5c1c0e10ee7e914b8a47cf8d1b3ae Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 20:34:29 +0200 Subject: [PATCH 298/992] R-3.2.0-goolf-1.7.20-bare.eb --- .../libjpeg-turbo-1.4.0-goolf-1.7.20.eb | 24 +++++++++++++++++ .../l/libpng/libpng-1.6.16-goolf-1.7.20.eb | 19 +++++++++++++ .../libreadline-6.3-goolf-1.7.20.eb | 27 +++++++++++++++++++ .../n/ncurses/ncurses-5.9-goolf-1.7.20.eb | 15 +++++++++++ .../r/R/R-3.2.0-goolf-1.7.20-bare.eb | 27 +++++++++++++++++++ 5 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..4197b7c635 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb new file mode 100644 index 0000000000..4132ab6f67 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb new file mode 100644 index 0000000000..5449121e0b --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb new file mode 100644 index 0000000000..a62ac8f668 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb @@ -0,0 +1,15 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, +and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and +function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb new file mode 100644 index 0000000000..d1098337a7 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' -- GitLab From c5624f2f880159ee7d66a5dc2ff4e05b41306e5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 20:53:43 +0200 Subject: [PATCH 299/992] fix tests w.r.t. external modules and Cray toolchains --- test/easyconfigs/easyconfigs.py | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5d7ca77279..4516a938ed 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -50,6 +50,7 @@ from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, proce from easybuild.tools import config from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version +from easybuild.tools.modules import modules_tool from easybuild.tools.robot import resolve_dependencies @@ -66,7 +67,9 @@ class EasyConfigTest(TestCase): config.init(eb_go.options, eb_go.get_options_by_section('config')) build_options = { 'check_osdeps': False, + 'external_modules_metadata': {}, 'force': True, + 'optarch': 'test', 'robot_path': get_paths_for("easyconfigs")[0], 'suffix_modules_path': GENERAL_CLASS, 'valid_module_classes': config.module_classes(), @@ -75,8 +78,14 @@ class EasyConfigTest(TestCase): config.init_build_options(build_options=build_options) config.set_tmpdir() del eb_go - + + # mock 'exist' and 'load' methods of modules tool, which are used for 'craype' external module + modtool = modules_tool() + modtool.exist = lambda m: [True]*len(m) + modtool.load = lambda m: True + log = fancylogger.getLogger("EasyConfigTest", fname=False) + # make sure a logger is present for main main._log = log ordered_specs = None @@ -93,6 +102,15 @@ class EasyConfigTest(TestCase): for spec in specs: self.parsed_easyconfigs.extend(process_easyconfig(spec)) + # filter out external modules + for ec in self.parsed_easyconfigs: + for dep in ec['dependencies'][:]: + if dep.get('external_module', False): + ec['dependencies'].remove(dep) + for dep in ec['unresolved_deps'][:]: + if dep.get('external_module', False): + ec['unresolved_deps'].remove(dep) + self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs) def test_dep_graph(self): -- GitLab From d6b1c83d0a70d80bccfe1a787b99d0cb18319df8 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 21:00:51 +0200 Subject: [PATCH 300/992] added NASM-2.11.06-goolf-1.7.20.eb --- .../n/NASM/NASM-2.11.06-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb new file mode 100644 index 0000000000..8ece8f5082 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From e8aa3700033275de4681eee55e4d20cd1271756f Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 21:01:47 +0200 Subject: [PATCH 301/992] changed java version to latest in 1.7.x branch --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb index d1098337a7..764ce77013 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_79', '', True), # Java bindings are built if Java is found, might as well provide it ] exts_list = [] -- GitLab From bc48592638f68af71e4c9d2acd19e9c0e95d056d Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 21:07:12 +0200 Subject: [PATCH 302/992] added Java-1.7.0_80.eb --- easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb new file mode 100644 index 0000000000..9acb602fa1 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.7.0_80' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 31327acc8bc46fae1fea637a2e1f68ad169273e5 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 21:23:43 +0200 Subject: [PATCH 303/992] bump java to 1.7.80 --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb index 764ce77013..ed4f2cd8f4 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_79', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] exts_list = [] -- GitLab From faa0b4476b12d727d2affcbff8243cb151e7458e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 22:24:55 +0200 Subject: [PATCH 304/992] {lang}[foss,intel/2015a] R 3.2.0 -bare --- .../r/R/R-3.2.0-foss-2015a-bare.eb | 27 +++++++++++++++++++ .../r/R/R-3.2.0-intel-2015a-bare.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb new file mode 100644 index 0000000000..db8d624ca1 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb new file mode 100644 index 0000000000..db8d624ca1 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' -- GitLab From 375755453436b11f29fc3335ce3279a32af04bcb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 22:30:36 +0200 Subject: [PATCH 305/992] also mention R v3.2.0 --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 2282d108e0..04333d14ff 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -19,7 +19,7 @@ v2.1.0 (April 28th 2015) - initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558) - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... - including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3, PETSc/SLEPc v3.5.3, WIEN2k v14.1 + including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1 - various other enhancements, including: - include 'pbr' dependency for 'lockfile' Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (#1462, #1540) - include SQLite as dependency in Python v2.7.9 easyconfigs (#1468) -- GitLab From 2dfba5a330f4b2a07a42565163342b800b570ba3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 22:36:55 +0200 Subject: [PATCH 306/992] fix toolchain in R easyconfig --- easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb index db8d624ca1..84e71410fa 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb @@ -5,7 +5,7 @@ versionsuffix = '-bare' homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] -- GitLab From 69f4fa55234443c3d9f2a7dbeb4f6453c4cd919a Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 22:40:57 +0200 Subject: [PATCH 307/992] R-3.2.0-goolf-1.7.20.eb --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 430 ++++++++++++++++++ 1 file changed, 430 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..a46bee15ff --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -0,0 +1,430 @@ +name = 'R' +version = '3.2.0' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.7.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.14', ext_options), + ('formatR', '1.1', ext_options), + ('gtools', '3.4.2', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.4.1', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.4', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-6', ext_options), + ('mclust', '5.0.0', ext_options), + ('RANN', '2.4.1', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.6-6', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-16', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.55.0-3', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.7', ext_options), + ('longitudinal', '1.1.11', ext_options), + ('checkmate', '1.5.2', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.11.3', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-9', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-4', ext_options), + ('stringr', '0.6.2', ext_options), + ('evaluate', '0.6', ext_options), + ('logspline', '2.1.5', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-3', ext_options), + ('plotrix', '3.5-11', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-31', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-0', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.5', ext_options), + ('RcppArmadillo', '0.4.650.1.1', ext_options), + ('plyr', '1.8.1', ext_options), + ('pROC', '1.7.3', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-40', ext_options), + ('tree', '1.0-35', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-12', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-9', ext_options), + ('nlme', '3.1-120', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('quantreg', '5.11', ext_options), + ('mgcv', '1.8-6', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-3', ext_options), + ('sp', '1.0-17', ext_options), + ('vcd', '1.3-2', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-9', ext_options), + ('mice', '2.22', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-15', ext_options), + ('mixtools', '1.0.2', ext_options), + ('cluster', '2.0.1', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-63', ext_options), + ('survival', '2.38-1', ext_options), + ('gam', '1.09.1', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-14', ext_options), + ('zoo', '1.7-12', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.22-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('lmtest', '0.9-33', ext_options), + ('mnormt', '1.5-2', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2012.9-1', ext_options), + ('lava', '1.4.0', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-3', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-9', ext_options), + ('VGAM', '0.9-7', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.11', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.1.33', ext_options), + ('R.utils', '2.0.0', ext_options), + ('R.matlab', '3.2.0', ext_options), + ('BiocGenerics', '0.12.1', 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('raster', '2.3-40', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '2.0-2', ext_options), + ('labdsv', '1.6-1', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.9', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('rms', '4.3-0', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', 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('AnnotationForge', '1.8.2', bioconductor_options), + ('KEGG.db', '3.0.0', bioconductor_options), + ('annaffy', '1.38.0', bioconductor_options), + ('gcrma', '2.38.0', bioconductor_options), + ('oligoClasses', '1.28.0', bioconductor_options), + ('edgeR', '3.8.6', bioconductor_options), + ('PFAM.db', '3.0.0', bioconductor_options), + ('locfit', '1.5-9.1', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('baySeq', '2.0.50', bioconductor_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('qvalue', '1.43.0', bioconductor_options), + ('impute', '1.40.0', bioconductor_options), + ('matrixStats', '0.14.0', ext_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.20.0', bioconductor_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('FactoMineR', '1.29', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-6', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('hgu133plus2.db', '3.0.0', bioconductor_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('illuminaio', '0.8.0', bioconductor_options), + ('registry', '0.2', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('bumphunter', '1.6.0', bioconductor_options), + ('multtest', '2.22.0', bioconductor_options), + ('siggenes', '1.40.0', bioconductor_options), + ('nleqslv', '2.7', ext_options), + ('DynDoc', '1.44.0', bioconductor_options), + ('genoset', '1.20.0', bioconductor_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.2', ext_options), + ('NOISeq', '2.8.0', bioconductor_options), + ('openxlsx', '2.4.0', ext_options), + ('Rgraphviz', '2.10.0', bioconductor_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('RNASeqPower', '1.6.0', bioconductor_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('XML', '3.98-1.1', ext_options), + ('biomaRt', '2.22.0', bioconductor_options), + ('annotate', '1.44.0', bioconductor_options), + ('GSEABase', '1.28.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('Category', '2.32.0', bioconductor_options), + ('org.Hs.eg.db', '3.0.0', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), + ('GOstats', '2.32.0', bioconductor_options), + ('rtracklayer', '1.26.3', bioconductor_options), + ('GenomicFeatures', '1.18.7', bioconductor_options), + ('BSgenome', '1.34.1', bioconductor_options), + ('VariantAnnotation', '1.12.9', bioconductor_options), + ('biovizBase', '1.14.1', bioconductor_options), + ('OrganismDbi', '1.8.1', bioconductor_options), + ('ggbio', '1.14.0', bioconductor_options), + ('geneplotter', '1.44.0', bioconductor_options), + ('DESeq2', '1.6.3', bioconductor_options), + ('ReportingTools', '2.6.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('affycoretools', '1.38.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.0.0', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.16.0', bioconductor_options), + ('GenomeGraphs', '1.26.0', bioconductor_options), + ('geneLenDataBase', '1.1.1', bioconductor_options), + ('goseq', '1.18.0', bioconductor_options), + ('httr', '0.6.1', ext_options), + ('KEGGREST', '1.6.4', bioconductor_options), + ('KEGGgraph', '1.24.0', bioconductor_options), + ('KEGGprofile', '1.8.2', bioconductor_options), + ('minfi', '1.12.0', bioconductor_options), + ('methylumi', '2.12.0', bioconductor_options), + ('lumi', '2.18.0', bioconductor_options), + ('widgetTools', '1.44.0', bioconductor_options), + ('tkWidgets', '1.44.0', bioconductor_options), + ('Mfuzz', '2.26.0', bioconductor_options), + ('maSigPro', '1.38.0', bioconductor_options), + ('SPIA', '2.18.0', bioconductor_options), + ('Gviz', '1.10.11', bioconductor_options), + ('cummeRbund', '2.8.2', bioconductor_options), + ('maptools', '0.8-34', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-0', ext_options), + ('goftest', '1.0-2', ext_options), + ('spatstat', '1.41-1', ext_options), + ('rgeos', '0.3-8', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('bio3d', '2.2-2', ext_options), + +] + +moduleclass = 'lang' -- GitLab From 9061990415ce599048a4c0954d7104b28ec77092 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 22:41:36 +0200 Subject: [PATCH 308/992] switched to java-1.7.0_80 --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index a46bee15ff..47aa361cd5 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] name_tmpl = '%(name)s_%(version)s.tar.gz' -- GitLab From edc13f8789fe70056b384b350618bdabca4a7bdf Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 22:56:40 +0200 Subject: [PATCH 309/992] libs updated 26-04-2015 --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 196 +++++++++--------- 1 file changed, 98 insertions(+), 98 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 47aa361cd5..3087ff6e51 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -73,21 +73,21 @@ exts_list = [ ('combinat', '0.0-8', ext_options), ('deal', '1.2-37', ext_options), ('fdrtool', '1.2.14', ext_options), - ('formatR', '1.1', ext_options), + ('formatR', '1.2', ext_options), ('gtools', '3.4.2', ext_options), ('gdata', '2.13.3', ext_options), ('GSA', '1.03', ext_options), - ('highr', '0.4.1', ext_options), + ('highr', '0.5', ext_options), ('infotheo', '1.2.0', ext_options), ('lars', '1.2', ext_options), ('lazy', '1.2-15', ext_options), ('kernlab', '0.9-20', ext_options), ('mime', '0.3', ext_options), - ('markdown', '0.7.4', ext_options), + ('markdown', '0.7.7', ext_options), ('mlbench', '2.1-1', ext_options), ('NLP', '0.1-6', ext_options), - ('mclust', '5.0.0', ext_options), - ('RANN', '2.4.1', ext_options), + ('mclust', '5.0.1', ext_options), + ('RANN', '2.5', ext_options), ('rmeta', '2.16', ext_options), ('segmented', '0.5-1.1', ext_options), ('som', '0.3-5', ext_options), @@ -119,7 +119,7 @@ exts_list = [ ('spam', '1.0-1', ext_options), ('subplex', '1.1-4', ext_options), ('stringr', '0.6.2', ext_options), - ('evaluate', '0.6', ext_options), + ('evaluate', '0.7', ext_options), ('logspline', '2.1.5', ext_options), ('ncbit', '2013.03.29', ext_options), ('permute', '0.8-3', ext_options), @@ -136,8 +136,8 @@ exts_list = [ ('Matrix', '1.2-0', ext_options), ('png', '0.1-7', ext_options), ('Rcpp', '0.11.5', ext_options), - ('RcppArmadillo', '0.4.650.1.1', ext_options), - ('plyr', '1.8.1', ext_options), + ('RcppArmadillo', '0.5.000.0', ext_options), + ('plyr', '1.8.2', ext_options), ('pROC', '1.7.3', ext_options), ('quadprog', '1.5-5', ext_options), ('BB', '2014.10-1', ext_options), @@ -158,7 +158,7 @@ exts_list = [ ('mgcv', '1.8-6', ext_options), ('colorspace', '1.2-6', ext_options), ('robustbase', '0.92-3', ext_options), - ('sp', '1.0-17', ext_options), + ('sp', '1.1-0', ext_options), ('vcd', '1.3-2', ext_options), ('snowfall', '1.84-6', ext_options), ('rpart', '4.1-9', ext_options), @@ -169,7 +169,7 @@ exts_list = [ ('akima', '0.5-11', ext_options), ('bitops', '1.0-6', ext_options), ('boot', '1.3-15', ext_options), - ('mixtools', '1.0.2', ext_options), + ('mixtools', '1.0.3', ext_options), ('cluster', '2.0.1', ext_options), ('gclus', '1.3.1', ext_options), ('coda', '0.17-1', ext_options), @@ -213,23 +213,23 @@ exts_list = [ ('R.methodsS3', '1.7.0', ext_options), ('R.oo', '1.19.0', ext_options), ('cgdsr', '1.1.33', ext_options), - ('R.utils', '2.0.0', ext_options), + ('R.utils', '2.0.1', ext_options), ('R.matlab', '3.2.0', ext_options), - ('BiocGenerics', '0.12.1', bioconductor_options), - ('Biobase', '2.26.0', bioconductor_options), - ('S4Vectors', '0.4.0', bioconductor_options), - ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.5', bioconductor_options), - ('AnnotationDbi', '1.28.2', bioconductor_options), - ('XVector', '0.6.0', bioconductor_options), - ('zlibbioc', '1.12.0', bioconductor_options), - ('Biostrings', '2.34.1', bioconductor_options), - ('GenomicRanges', '1.18.4', bioconductor_options), - ('Rsamtools', '1.18.3', bioconductor_options), - ('BiocParallel', '1.0.3', bioconductor_options), - ('GenomicAlignments', '1.2.2', bioconductor_options), - ('ShortRead', '1.24.0', bioconductor_options), - ('graph', '1.44.1', bioconductor_options), + ('BiocGenerics', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.0', bioconductor_options), + ('IRanges', '2.2.1', bioconductor_options), + ('GenomeInfoDb', '1.4.0', bioconductor_options), + ('AnnotationDbi', '1.30.0', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.0', bioconductor_options), + ('GenomicRanges', '1.20.3', bioconductor_options), + ('Rsamtools', '1.20.1', bioconductor_options), + ('BiocParallel', '1.2.0', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), ('gbm', '2.1.1', ext_options), ('dichromat', '2.0-0', ext_options), ('Formula', '1.2-1', ext_options), @@ -277,7 +277,7 @@ exts_list = [ ('glmnet', '2.0-2', ext_options), ('labdsv', '1.6-1', ext_options), ('MatrixModels', '0.4-0', ext_options), - ('stabs', '0.5-1', ext_options), + ('stabs', '0.5-1', ext_options), ('mboost', '2.4-2', ext_options), ('msm', '1.5', ext_options), ('nor1mix', '1.2-0', ext_options), @@ -296,7 +296,7 @@ exts_list = [ ('chemometrics', '1.3.9', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-4', ext_options), - ('knitr', '1.9', ext_options), + ('knitr', '1.10', ext_options), ('statmod', '1.4.21', ext_options), ('miscTools', '0.6-16', ext_options), ('maxLik', '1.2-4', ext_options), @@ -306,33 +306,33 @@ exts_list = [ ('reshape', '0.8.5', ext_options), ('optparse', '1.3.0', ext_options), ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), # requires R-3.1.1 or higher - ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), - ('preprocessCore', '1.28.0', bioconductor_options), - ('affy', '1.44.0', bioconductor_options), - ('GO.db', '3.0.0', bioconductor_options), - ('limma', '3.22.7', bioconductor_options), - ('RBGL', '1.42.0', bioconductor_options), - ('org.Hs.eg.db', '3.0.0', bioconductor_options), - ('AnnotationForge', '1.8.2', bioconductor_options), - ('KEGG.db', '3.0.0', bioconductor_options), - ('annaffy', '1.38.0', bioconductor_options), - ('gcrma', '2.38.0', bioconductor_options), - ('oligoClasses', '1.28.0', bioconductor_options), - ('edgeR', '3.8.6', bioconductor_options), - ('PFAM.db', '3.0.0', bioconductor_options), + ('neuRosim', '0.2-12', ext_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.1', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.0', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.1', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.0', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.0', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), ('locfit', '1.5-9.1', ext_options), ('gridExtra', '0.9.1', ext_options), ('GGally', '0.5.0', ext_options), - ('baySeq', '2.0.50', bioconductor_options), + ('baySeq', '2.2.0', bioconductor_options), ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), - ('qvalue', '1.43.0', bioconductor_options), - ('impute', '1.40.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), ('matrixStats', '0.14.0', ext_options), ('samr', '2.0', ext_options), - ('DEGseq', '1.20.0', bioconductor_options), + ('DEGseq', '1.22.0', bioconductor_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), @@ -345,76 +345,76 @@ exts_list = [ ('trimcluster', '0.1-2', ext_options), ('fpc', '2.1-9', ext_options), ('BiasedUrn', '1.06.1', ext_options), - ('hgu133plus2.db', '3.0.0', bioconductor_options), + ('hgu133plus2.db', '3.1.2', bioconductor_options), ('TeachingDemos', '2.9', ext_options), ('jsonlite', '0.9.16', ext_options), ('kohonen', '2.0.18', ext_options), ('base64', '1.1', ext_options), - ('illuminaio', '0.8.0', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), ('registry', '0.2', ext_options), ('pkgmaker', '0.22', ext_options), ('rngtools', '1.2.4', ext_options), ('doRNG', '1.6', ext_options), - ('bumphunter', '1.6.0', bioconductor_options), - ('multtest', '2.22.0', bioconductor_options), - ('siggenes', '1.40.0', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), ('nleqslv', '2.7', ext_options), - ('DynDoc', '1.44.0', bioconductor_options), - ('genoset', '1.20.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '1.0.2', ext_options), - ('NOISeq', '2.8.0', bioconductor_options), + ('NOISeq', '2.10.0', bioconductor_options), ('openxlsx', '2.4.0', ext_options), - ('Rgraphviz', '2.10.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), ('pvclust', '1.3-2', ext_options), ('RCircos', '1.1.2', ext_options), - ('RNASeqPower', '1.6.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('XML', '3.98-1.1', ext_options), - ('biomaRt', '2.22.0', bioconductor_options), - ('annotate', '1.44.0', bioconductor_options), - ('GSEABase', '1.28.0', bioconductor_options), - ('genefilter', '1.48.1', bioconductor_options), - ('Category', '2.32.0', bioconductor_options), - ('org.Hs.eg.db', '3.0.0', bioconductor_options), - ('AnnotationForge', '1.8.2', bioconductor_options), - ('GOstats', '2.32.0', bioconductor_options), - ('rtracklayer', '1.26.3', bioconductor_options), - ('GenomicFeatures', '1.18.7', bioconductor_options), - ('BSgenome', '1.34.1', bioconductor_options), - ('VariantAnnotation', '1.12.9', bioconductor_options), - ('biovizBase', '1.14.1', bioconductor_options), - ('OrganismDbi', '1.8.1', bioconductor_options), - ('ggbio', '1.14.0', bioconductor_options), - ('geneplotter', '1.44.0', bioconductor_options), - ('DESeq2', '1.6.3', bioconductor_options), - ('ReportingTools', '2.6.0', bioconductor_options), - ('genefilter', '1.48.1', bioconductor_options), - ('affycoretools', '1.38.0', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.0.0', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('annotate', '1.46.0', bioconductor_options), + ('GSEABase', '1.30.1', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.0', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('rtracklayer', '1.28.2', bioconductor_options), + ('GenomicFeatures', '1.20.0', bioconductor_options), + ('BSgenome', '1.36.0', bioconductor_options), + ('VariantAnnotation', '1.14.0', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.0', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.0', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('affycoretools', '1.40.1', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), ('Homo.sapiens', '1.1.2', bioconductor_options), ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), - ('AgiMicroRna', '2.16.0', bioconductor_options), - ('GenomeGraphs', '1.26.0', bioconductor_options), - ('geneLenDataBase', '1.1.1', bioconductor_options), - ('goseq', '1.18.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), ('httr', '0.6.1', ext_options), - ('KEGGREST', '1.6.4', bioconductor_options), - ('KEGGgraph', '1.24.0', bioconductor_options), - ('KEGGprofile', '1.8.2', bioconductor_options), - ('minfi', '1.12.0', bioconductor_options), - ('methylumi', '2.12.0', bioconductor_options), - ('lumi', '2.18.0', bioconductor_options), - ('widgetTools', '1.44.0', bioconductor_options), - ('tkWidgets', '1.44.0', bioconductor_options), - ('Mfuzz', '2.26.0', bioconductor_options), - ('maSigPro', '1.38.0', bioconductor_options), - ('SPIA', '2.18.0', bioconductor_options), - ('Gviz', '1.10.11', bioconductor_options), - ('cummeRbund', '2.8.2', bioconductor_options), - ('maptools', '0.8-34', ext_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.1', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.0', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), + ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), ('tensor', '1.5', ext_options), ('polyclip', '1.3-0', ext_options), -- GitLab From cf2b5fee068415b589f0d9527298265dd6061607 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2015 09:07:35 +0200 Subject: [PATCH 310/992] enable retain_all_deps when resolving dependencies in easyconfig tests --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4516a938ed..838f4a2957 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -111,7 +111,7 @@ class EasyConfigTest(TestCase): if dep.get('external_module', False): ec['unresolved_deps'].remove(dep) - self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs) + self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, retain_all_deps=True) def test_dep_graph(self): """Unit test that builds a full dependency graph.""" -- GitLab From ae9df0b0abcbe10010b17f04f2fc7150f67d318a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2015 10:12:58 +0200 Subject: [PATCH 311/992] bump version of libpng in R 3.2.0 easyconfigs --- .../l/libpng/libpng-1.6.17-foss-2015a.eb | 19 +++++++++++++++++++ .../l/libpng/libpng-1.6.17-goolf-1.7.20.eb | 19 +++++++++++++++++++ .../l/libpng/libpng-1.6.17-intel-2015a.eb | 19 +++++++++++++++++++ .../r/R/R-3.2.0-foss-2015a-bare.eb | 2 +- .../r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- .../r/R/R-3.2.0-intel-2015a-bare.eb | 2 +- 6 files changed, 60 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb new file mode 100644 index 0000000000..2519d4c46d --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb new file mode 100644 index 0000000000..8e90204af6 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb new file mode 100644 index 0000000000..afab7cb441 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb index 84e71410fa..6cf2221cfd 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb @@ -17,7 +17,7 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R + ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb index ed4f2cd8f4..d8c3392f6a 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -17,7 +17,7 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R + ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb index db8d624ca1..f4f7ec9970 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb @@ -17,7 +17,7 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R + ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] -- GitLab From f557d3632c2e91a1994df55434463f61f1cf4b83 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Mon, 27 Apr 2015 11:08:19 +0200 Subject: [PATCH 312/992] updated to latest libpng --- .../l/libpng/libpng-1.6.17-goolf-1.7.20.eb | 19 +++++++++++++++++++ .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb new file mode 100644 index 0000000000..8e90204af6 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 3087ff6e51..93ecdc515d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -17,7 +17,7 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R + ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] -- GitLab From 988a11260662f2b1b7bea3aca07847272cc56535 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Mon, 27 Apr 2015 11:14:38 +0200 Subject: [PATCH 313/992] removed libpng easyconfig which is already in develop --- .../l/libpng/libpng-1.6.17-goolf-1.7.20.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb deleted file mode 100644 index 8e90204af6..0000000000 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpng' -version = '1.6.17' - -homepage = 'http://www.libpng.org/pub/png/libpng.html' -description = "libpng is the official PNG reference library" - -toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('zlib', '1.2.8')] - -configopts = "--with-pic" - -moduleclass = 'lib' -- GitLab From 3af0e7c932393ffdd18b5915d2fc087280fb0986 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2015 10:27:27 +0200 Subject: [PATCH 314/992] fix date and counts in release notes --- RELEASE_NOTES | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 04333d14ff..737619aa4f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,12 +3,13 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,344 easyconfig files, for 608 different software packages, +The latest version of easybuild-easyconfig provides 3,617 easyconfig files, for 608 different software packages, 33 different (compiler) toolchains and 8 software bundles. -v2.1.0 (April 28th 2015) +v2.1.0 (April 30th 2015) ------------------------ +feature + bugfix release - added example easyconfig files for 27 new software packages: AFNI (#1322, #1521), BCFtools (#1492), getdp (#1518), gmsh (#1518), gtest (#1244), hanythingondemand (#1530), mawk (#1369), Minimac (#815), Minimac3 (#1502), monty (#1548), Octave (#1563), pbs_python (#1530), pigz (#1036), -- GitLab From d952c5b7d9d733b1ef5d8a90d7f4d9ea828432db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2015 10:45:47 +0200 Subject: [PATCH 315/992] fix long line --- RELEASE_NOTES | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 737619aa4f..84c44e6c5f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -49,7 +49,8 @@ feature + bugfix release rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), ZPAQ (#1242) - added easyconfigs for new (common) toolchains - foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) + foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), + intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) - added new software bundle: Autotools (#1385) - various other enhancements, including: - don't define $LDSHARED in zlib easyconfigs (#1350) -- GitLab From 9276b84095c3561e9114abfda2155cdcd8656124 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 28 Apr 2015 17:10:06 +0200 Subject: [PATCH 316/992] Adjusted Cube download URL and tweaked build Requires https://github.com/hpcugent/easybuild-easyblocks/pull/552 --- .../c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index a097385484..cd8e278f30 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -20,19 +20,21 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] patches = ['Cube-4.2_fix-Qt-version-check.patch'] dependencies = [('Qt', '4.8.4')] -configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" - sanity_check_paths = { 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], 'dirs': ["include/cube", "include/cubew"], } +# If all prerequisites for the Cube Java reader are available on the system, +# parallel builds will fail. Alternatively, disable the Java reader using +# configopts = "--without-java-reader" +maxparallel = 1 + moduleclass = 'perf' -- GitLab From d8c294bcd0f997894d59d977a998c975727b5f6d Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 28 Apr 2015 18:31:22 +0200 Subject: [PATCH 317/992] Adjusted Scalasca URL --- .../s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb index 1f62732cc1..b4c09a0c49 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb @@ -26,9 +26,8 @@ dependencies = [ ('OTF2', '1.2.1'), ] -# http://apps.fz-juelich.de/scalasca/releases/scalasca/2.0/dist/scalasca-2.0.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/2.0/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] sanity_check_paths = { 'files': ["bin/scalasca", ("lib64/libpearl.replay.a", "lib/libpearl.replay.a")], -- GitLab From 1b9d0beacdeccd8e77ac617239aae93598f7afa4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2015 07:46:01 +0200 Subject: [PATCH 318/992] include link to EB@Cray wiki page --- RELEASE_NOTES | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 84c44e6c5f..31240be8e3 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -18,6 +18,7 @@ feature + bugfix release Xmipp (#1489) - added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE - initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558) + - see also https://github.com/hpcugent/easybuild/wiki/EasyBuild-on-Cray - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1 @@ -27,7 +28,7 @@ feature + bugfix release - set $LD_PRELOAD for Hoard and jemalloc (#1470) - fix homepage in SCOTCH easyconfigs (#1485) - adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510) - - enable pic option in expat easyconfigs (#1562) + - enable pic toolchain option in expat easyconfigs (#1562) - extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (#1568) - various bug fixes, including: - adding missing zlib dependency in all Tcl easyconfig files (#1344) -- GitLab From a67f2a824517e5587b88992dfb75135988593f00 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 29 Apr 2015 10:18:54 +0200 Subject: [PATCH 319/992] Try to fix build issue by patching `configure` Provide updated easyconfig for Cube 4.3 (which should be used anyhow) --- .../c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 19 +- .../c/Cube/Cube-4.2_fix-with-qt-check.patch | 209 ++++++++++++++++++ .../c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb | 40 ++++ 3 files changed, 261 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index cd8e278f30..b578e14673 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -1,6 +1,7 @@ # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr +# Authors:: Markus Geimer # License:: New BSD # # This work is based from experiences from the UNITE project @@ -23,18 +24,22 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -patches = ['Cube-4.2_fix-Qt-version-check.patch'] +patches = [ + 'Cube-4.2_fix-Qt-version-check.patch', + 'Cube-4.2_fix-with-qt-check.patch', +] dependencies = [('Qt', '4.8.4')] +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support is has difficulties handling +# parallel builds. +configopts = "--without-java-reader" + sanity_check_paths = { 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], 'dirs': ["include/cube", "include/cubew"], } -# If all prerequisites for the Cube Java reader are available on the system, -# parallel builds will fail. Alternatively, disable the Java reader using -# configopts = "--without-java-reader" -maxparallel = 1 - moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch b/easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch new file mode 100644 index 0000000000..5ea89bb644 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch @@ -0,0 +1,209 @@ +--- build-backend/configure.orig 2013-08-02 13:20:33.000000000 +0200 ++++ build-backend/configure 2015-04-29 09:56:00.891697331 +0200 +@@ -19819,6 +19819,8 @@ $as_echo "$at_darwin" >&6; } + + # Find qmake. + ++ if test "x$QT_PATH" == "x"; then : ++ + for ac_prog in qmake-qt4 qmake + do + # Extract the first word of "$ac_prog", so it can be a program name with args. +@@ -19867,6 +19869,57 @@ done + test -n "$QMAKE" || QMAKE="missing" + + ++else ++ ++ for ac_prog in qmake ++do ++ # Extract the first word of "$ac_prog", so it can be a program name with args. ++set dummy $ac_prog; ac_word=$2 ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 ++$as_echo_n "checking for $ac_word... " >&6; } ++if ${ac_cv_path_QMAKE+:} false; then : ++ $as_echo_n "(cached) " >&6 ++else ++ case $QMAKE in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_QMAKE="$QMAKE" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++as_dummy="$QT_PATH:$QT_DIR:$PATH:$tmp_qt_paths" ++for as_dir in $as_dummy ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_QMAKE="$as_dir/$ac_word$ac_exec_ext" ++ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++ done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++QMAKE=$ac_cv_path_QMAKE ++if test -n "$QMAKE"; then ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $QMAKE" >&5 ++$as_echo "$QMAKE" >&6; } ++else ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 ++$as_echo "no" >&6; } ++fi ++ ++ ++ test -n "$QMAKE" && break ++done ++test -n "$QMAKE" || QMAKE="missing" ++ ++ ++fi + if test x"$QMAKE" = xmissing; then + as_fn_error $? "Cannot find qmake in your PATH. Try to specify the exact path using the option --with-qt= or to switch off the compilation of gui using option --without-gui." "$LINENO" 5 + break +@@ -20309,7 +20362,59 @@ $as_echo "$at_cv_qt_build" >&6; } + + # Find moc (Meta Object Compiler). + +- for ac_prog in moc-qt4 moc ++ if test "x$QT_PATH" == "x"; then : ++ ++ for ac_prog in moc-qt4 moc ++do ++ # Extract the first word of "$ac_prog", so it can be a program name with args. ++set dummy $ac_prog; ac_word=$2 ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 ++$as_echo_n "checking for $ac_word... " >&6; } ++if ${ac_cv_path_MOC+:} false; then : ++ $as_echo_n "(cached) " >&6 ++else ++ case $MOC in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_MOC="$MOC" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++as_dummy="$PATH:$tmp_qt_paths" ++for as_dir in $as_dummy ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_MOC="$as_dir/$ac_word$ac_exec_ext" ++ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++ done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++MOC=$ac_cv_path_MOC ++if test -n "$MOC"; then ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MOC" >&5 ++$as_echo "$MOC" >&6; } ++else ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 ++$as_echo "no" >&6; } ++fi ++ ++ ++ test -n "$MOC" && break ++done ++test -n "$MOC" || MOC="missing" ++ ++ ++else ++ ++ for ac_prog in moc + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -20356,6 +20461,8 @@ fi + done + test -n "$MOC" || MOC="missing" + ++ ++fi + if test x"$MOC" = xmissing; then + as_fn_error $? "Cannot find moc (Meta Object Compiler) in your PATH. Try using --with-qt." "$LINENO" 5 + break +@@ -20364,7 +20471,59 @@ test -n "$MOC" || MOC="missing" + + # Find uic (User Interface Compiler). + +- for ac_prog in uic-qt4 uic ++ if test "x$QT_PATH" == "x"; then : ++ ++ for ac_prog in uic-qt4 uic ++do ++ # Extract the first word of "$ac_prog", so it can be a program name with args. ++set dummy $ac_prog; ac_word=$2 ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 ++$as_echo_n "checking for $ac_word... " >&6; } ++if ${ac_cv_path_UIC+:} false; then : ++ $as_echo_n "(cached) " >&6 ++else ++ case $UIC in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_UIC="$UIC" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++as_dummy="$PATH:$tmp_qt_paths" ++for as_dir in $as_dummy ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_UIC="$as_dir/$ac_word$ac_exec_ext" ++ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++ done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++UIC=$ac_cv_path_UIC ++if test -n "$UIC"; then ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $UIC" >&5 ++$as_echo "$UIC" >&6; } ++else ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 ++$as_echo "no" >&6; } ++fi ++ ++ ++ test -n "$UIC" && break ++done ++test -n "$UIC" || UIC="missing" ++ ++ ++else ++ ++ for ac_prog in uic + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -20411,6 +20570,8 @@ fi + done + test -n "$UIC" || UIC="missing" + ++ ++fi + if test x"$UIC" = xmissing; then + as_fn_error $? "Cannot find uic (User Interface Compiler) in your PATH. Try using --with-qt." "$LINENO" 5 + break diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..0a2aec777e --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Authors:: Markus Geimer +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'EB_Score_minus_P' + +name = "Cube" +version = "4.3" + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +dependencies = [('Qt', '4.8.4')] + +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support is has difficulties handling +# parallel builds. +configopts = "--without-java-reader" + +sanity_check_paths = { + 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' -- GitLab From 2b2dcd9e93940f02ad86d23d851fcdd74d65e6b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2015 10:54:06 +0200 Subject: [PATCH 320/992] include patch for Python 2.5.6 to fix issue with newer versions of 'svnversion' command that spits out 'Unversioned directory' rather than 'exported' --- .../Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 2 ++ .../Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 2 ++ .../p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 2 ++ .../p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 2 ++ .../p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 2 ++ .../p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 2 ++ .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 2 ++ .../p/Python/Python-2.5.6_svnversion-cmd.patch | 12 ++++++++++++ 8 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index a0f450f70f..43ff3feba7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index 53b6064132..f825fd87bd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index ed1944c3f2..18d0d4a8df 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index d9118da106..5cad1244b7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + patches = ['python_libffi_int128_icc.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index da9bd1c2a4..eecf1e2276 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + patches = ['python_libffi_int128_icc.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index ae0e9d0e08..0228eae5be 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index 6d976f526f..fc44c37e78 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch new file mode 100644 index 0000000000..eef94268d9 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch @@ -0,0 +1,12 @@ +--- Python-2.5.6/configure.orig 2015-04-29 10:40:05.254502098 +0200 ++++ Python-2.5.6/configure 2015-04-29 10:42:01.739388944 +0200 +@@ -4242,7 +4242,8 @@ + + if test $SVNVERSION = found + then +- SVNVERSION="svnversion \$(srcdir)" ++ #SVNVERSION="svnversion \$(srcdir)" ++ SVNVERSION="echo exported" + else + SVNVERSION="echo exported" + fi -- GitLab From 0a8c2c2c2df86ed790eee92024a2dc1ce8ac08fb Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 29 Apr 2015 11:17:57 +0200 Subject: [PATCH 321/992] Add comment that patches are no longer required for Cube 4.2.2 and up --- easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index b578e14673..941a048ad1 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -24,6 +24,7 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +# Backported fixes included in Cube 4.2.2 and up patches = [ 'Cube-4.2_fix-Qt-version-check.patch', 'Cube-4.2_fix-with-qt-check.patch', -- GitLab From 454e95a3227952c3e1d4743bf5882af4644e303e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 29 Apr 2015 12:25:43 +0200 Subject: [PATCH 322/992] dummy --- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From 995c8f51d24a0ee8950f96471e01d87b18d54226 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 29 Apr 2015 12:34:10 +0200 Subject: [PATCH 323/992] HMMER 3.1b2 with intel-2015a --- .../h/HMMER/HMMER-3.1b2-intel-2015a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index e69de29bb2..5255f85ddc 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.1b2' + +homepage = 'http://hmmer.janelia.org/' +description = """HMMER is used for searching sequence databases for homologs of protein sequences, + and for making protein sequence alignments. It implements methods using probabilistic models + called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other + sequence alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote homologs + because of the strength of its underlying mathematical models. In the past, this strength + came at significant computational expense, but in the new HMMER3 project, HMMER is now + essentially as fast as BLAST.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +source_urls = ['http://selab.janelia.org/software/hmmer%(version_major)s/%(version)s/'] + +installopts = ' && cd easel && make install' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", + "esl-alimap", "esl-cluster", "esl-mask"]], + 'dirs': [] +} + +runtest = 'check' + +moduleclass = 'bio' -- GitLab From 5da3932cb8ae56f330d05e98c9406cc155a4d4a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2015 22:36:23 +0200 Subject: [PATCH 324/992] include PR #1574 in release notes --- RELEASE_NOTES | 2 ++ 1 file changed, 2 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 31240be8e3..9cda838d2c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -38,6 +38,8 @@ feature + bugfix release - replace use of $root with %(installdir)s to ensure compatibility with module files in Lua syntax (#1532) - stop relying on $MKLROOT in ROOT easyconfigs (#1537) - use proper Bundle easyblock for biodeps/PRACE (#1566) + - make source_urls in Cube and Scalasca easyconfigs compatible with --try-software-version (#1574) + - add patch for Cube to fix configure script w.r.t. Qt dependency, add --without-java-reader configure option (#1574) v2.0.0 (March 6th 2015) ----------------------- -- GitLab From 1272d0e0570333f0a362b1d8dbe751cc64cfb14a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 08:54:20 +0200 Subject: [PATCH 325/992] fix easyconfigs count --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 9cda838d2c..c00535497a 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,617 easyconfig files, for 608 different software packages, +The latest version of easybuild-easyconfig provides 3,618 easyconfig files, for 608 different software packages, 33 different (compiler) toolchains and 8 software bundles. v2.1.0 (April 30th 2015) -- GitLab From e0027ca8d8c3107c6588145867e4532484017d25 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 30 Apr 2015 08:56:53 +0200 Subject: [PATCH 326/992] Dummy --- easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From 89f4e4170a0685beececd12fc9bf083377ade19e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 30 Apr 2015 09:53:25 +0200 Subject: [PATCH 327/992] eudev 1st try --- .../e/eudev/eudev-3.0-intel-2014b.eb | 31 +++++++++++++++++++ .../e/eudev/eudev-3.0_pre-2.6.34_kernel.patch | 16 ++++++++++ .../g/gperf/gperf-3.0.4-intel-2014b.eb | 23 ++++++++++++++ 3 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb index e69de29bb2..b64ac043f3 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.0' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-%(version)s_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +preinstallopts = "make check && " + +sanity_check_paths = { + 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs' : [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch b/easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch new file mode 100644 index 0000000000..7fb7da7902 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch @@ -0,0 +1,16 @@ +#inspiration from http://repository.timesys.com/buildsources/u/udev/udev-181/udev-181-define-trigger-happy.patch +#BTN_TRIGGER_HAPPY is not defined in /usr/include/linux/input.h for pre 2.6.34 kernels +# B. Hajgato April 30 2015 +--- eudev-3.0/src/udev/udev-builtin-input_id.c.org 2015-04-30 09:11:07.990269206 +0200 ++++ eudev-3.0/src/udev/udev-builtin-input_id.c 2015-04-30 09:12:19.407272116 +0200 +@@ -33,6 +33,10 @@ + #include "udev.h" + #include "util.h" + ++#ifndef BTN_TRIGGER_HAPPY ++#define BTN_TRIGGER_HAPPY 0x2c0 ++#endif ++ + /* we must use this kernel-compatible implementation */ + #define BITS_PER_LONG (sizeof(unsigned long) * 8) + #define NBITS(x) ((((x)-1)/BITS_PER_LONG)+1) diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb new file mode 100644 index 0000000000..bef0d843d8 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] + } + +moduleclass = 'devel' -- GitLab From 80e714ed681c330694fbf27ab62462db2ab04ce7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 13:36:11 +0200 Subject: [PATCH 328/992] bump version to v2.1.x --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 5b55ee3e55..e89248dca4 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.1.0' +VERSION = '2.1.1dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 172dc89ec881e00da3be3a32b133013bc46769b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 16:06:57 +0200 Subject: [PATCH 329/992] bump version to v2.2.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index e89248dca4..9e5dd5137c 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.1.1dev' +VERSION = '2.2.0dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 0a603f9b0f666e4127d34e8b6b1686c27979ee7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:18:35 +0200 Subject: [PATCH 330/992] add easyconfig file for EasyBuild v2.1.0 --- .../e/EasyBuild/EasyBuild-2.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb new file mode 100644 index 0000000000..d753a18457 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = "2.1.0" + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/v/vsc-base/', + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.0.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From bd4e4c8b7189166116c41cced62fd385e1872741 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:19:52 +0200 Subject: [PATCH 331/992] style fix --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index d753a18457..b11b8ff6c1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' -version = "2.1.0" +version = '2.1.0' homepage = 'http://hpcugent.github.com/easybuild/' description = """EasyBuild is a software build and installation framework -- GitLab From f7adb79305616713b1d28b24b466e84669642750 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 4 May 2015 09:49:11 +0200 Subject: [PATCH 332/992] BLAST+ with foss 2015a --- .../BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..37178f8aa5 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = "2.2.30" +versionsuffix = '-Python-2.7.9' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = ['%(name)s-%(version)s_basename-fixes.patch'] + +dependencies = [('Boost', '1.57.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' + -- GitLab From 64389a02f3dfaec9bf1cb98ea088df5d96e98d36 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2015 00:34:47 +0300 Subject: [PATCH 333/992] {geo}[foss/2015a] WRF 3.6.1 --- .../b/Bison/Bison-3.0.2-foss-2015a.eb | 22 ++++++++++ .../c/CMake/CMake-3.0.0-foss-2015a.eb | 22 ++++++++++ .../c/cURL/cURL-7.37.1-foss-2015a.eb | 27 +++++++++++++ .../d/Doxygen/Doxygen-1.8.7-foss-2015a.eb | 18 +++++++++ .../f/flex/flex-2.5.39-foss-2015a.eb | 14 +++++++ .../h/HDF5/HDF5-1.8.13-foss-2015a.eb | 25 ++++++++++++ .../j/JasPer/JasPer-1.900.1-foss-2015a.eb | 21 ++++++++++ .../easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb | 23 +++++++++++ .../netCDF-Fortran-4.4.0-foss-2015a.eb | 17 ++++++++ .../n/netCDF/netCDF-4.3.2-foss-2015a.eb | 31 ++++++++++++++ .../t/tcsh/tcsh-6.18.01-foss-2015a.eb | 38 ++++++++++++++++++ .../w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb | 40 +++++++++++++++++++ 12 files changed, 298 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb new file mode 100644 index 0000000000..0b270e9381 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb new file mode 100644 index 0000000000..c55a48656c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb new file mode 100644 index 0000000000..0ba45ba9e5 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.37.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb new file mode 100644 index 0000000000..6fae2382dd --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.7' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb new file mode 100644 index 0000000000..f9226ff5f3 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb new file mode 100644 index 0000000000..f79d365b61 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.13' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb new file mode 100644 index 0000000000..02cb1d4f4c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb new file mode 100644 index 0000000000..411820a76b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb new file mode 100644 index 0000000000..d623122642 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb @@ -0,0 +1,17 @@ +name = 'netCDF-Fortran' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.3.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb new file mode 100644 index 0000000000..8319de8066 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb @@ -0,0 +1,31 @@ +name = 'netCDF' +version = '4.3.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] + +dependencies = [('HDF5', '1.8.13')] + +builddependencies = [ + ('CMake', '3.0.0'), + ('Doxygen', '1.8.7'), + ('cURL', '7.37.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb new file mode 100644 index 0000000000..4b5f7237ff --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb new file mode 100644 index 0000000000..5e773ca4e8 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb @@ -0,0 +1,40 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_netCDF-Fortran_separate_path.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' -- GitLab From 638cc7d093d42f9d64b55820f73c2dd75391b28a Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Tue, 5 May 2015 16:00:36 +0200 Subject: [PATCH 334/992] Adding the easyconfigs for ictce-7.3.5 --- easybuild/easyconfigs/i/icc/icc-2015.3.187.eb | 17 ++++++++++++++ .../i/iccifort/iccifort-2015.3.187.eb | 16 ++++++++++++++ easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb | 21 ++++++++++++++++++ .../easyconfigs/i/ifort/ifort-2015.3.187.eb | 17 ++++++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb | 18 +++++++++++++++ .../i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb | 22 +++++++++++++++++++ .../impi-5.0.3.048-iccifort-2015.3.187.eb | 19 ++++++++++++++++ 7 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/i/icc/icc-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb new file mode 100644 index 0000000000..55dec91be5 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'icc' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_ccompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb new file mode 100644 index 0000000000..8387432380 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb @@ -0,0 +1,16 @@ +easyblock = "Toolchain" + +name = 'iccifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version), + ('ifort', version), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb new file mode 100644 index 0000000000..6190ed2906 --- /dev/null +++ b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'ictce' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '3.187' +compver = '2015.%s' % suff + +dependencies = [ # version/released + ('icc', compver), # Apr 13th 2015 + ('ifort', compver), # Apr 13th 2015 + ('impi', '5.0.3.048', '', ('iccifort', compver)), # Feb 10th 2015 + ('imkl', '11.2.%s' % suff, '', ('iimpi', version)), # Apr 13th 2015 +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb new file mode 100644 index 0000000000..8253a3390b --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'ifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_fcompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb new file mode 100644 index 0000000000..b0fe67cb26 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb @@ -0,0 +1,18 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2015.3.187' +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '5.0.3.048', '', ('iccifort', compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb new file mode 100644 index 0000000000..807b5f2004 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.2.3.187' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '7.3.5'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb new file mode 100644 index 0000000000..5e0972d8f3 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '5.0.3.048' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2015.3.187'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' -- GitLab From 26de6e35ca028edfc16dbf44ec58e1858b45e426 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 May 2015 18:36:05 +0200 Subject: [PATCH 335/992] Boost 1.58 for intel/2015a --- .../Boost-1.58.0-intel-2015a-Python-2.7.9.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..a209577bba --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 3568cde808c6d65622e0581414372da7c1ffd687 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 May 2015 18:37:17 +0200 Subject: [PATCH 336/992] Boost 1.58.0 for foss/2015a --- .../Boost-1.58.0-foss-2015a-Python-2.7.9.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..bbef8b760b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From d30c3bb38f9bc53bd6f1145854607c759ccf0ac7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 6 May 2015 10:23:17 +0200 Subject: [PATCH 337/992] Minor corrections --- easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb index bef0d843d8..d44084ea5c 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb @@ -9,15 +9,14 @@ description = """GNU gperf is a perfect hash function generator. For a given lis function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.""" - toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/gperf'], - 'dirs': [] - } + 'files': ['bin/gperf'], + 'dirs': [] +} moduleclass = 'devel' -- GitLab From abee1f0f0dd2f23cdb08bb9aaeb504a80ea11d6f Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Wed, 6 May 2015 11:31:15 +0200 Subject: [PATCH 338/992] Adding HPL 2.1 with ictce-7.3.5 --- .../easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb new file mode 100644 index 0000000000..55ab924d7d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 633e68830ef8be546092e0d16857af624dfe44b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 May 2015 15:59:13 +0300 Subject: [PATCH 339/992] enable usempi in GROMACS Cray easyconfig, the easyblock enables MPI support on it --- .../easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb index c7618bc1f3..1aa3886405 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb @@ -19,6 +19,7 @@ description = """GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz source_urls = [ -- GitLab From b9f89c0d31ee7e48beac5dcb6e6383313d9ed13d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:18:35 +0200 Subject: [PATCH 340/992] add easyconfig file for EasyBuild v2.1.0 --- .../e/EasyBuild/EasyBuild-2.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb new file mode 100644 index 0000000000..d753a18457 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = "2.1.0" + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/v/vsc-base/', + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.0.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 8ab052fa8bfff470f7e635ae25fc48d555dcfaa9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:19:52 +0200 Subject: [PATCH 341/992] style fix --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index d753a18457..b11b8ff6c1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' -version = "2.1.0" +version = '2.1.0' homepage = 'http://hpcugent.github.com/easybuild/' description = """EasyBuild is a software build and installation framework -- GitLab From c834c42978d09f4ada1be3fc9ef552c6c74d6f5b Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 09:42:44 +0200 Subject: [PATCH 342/992] added even newer cutadapt --- ...cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..1c463c28a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.8.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt',], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From c1a99608bf96df972dc4e1b30ee639db3bae71f5 Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 09:56:11 +0200 Subject: [PATCH 343/992] fixed filename --- ...b-Python-2.7.8.eb => cutadapt-1.5-intel-2014b-Python-2.7.8.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/cutadapt/{cutadapt-1.5-intel2014b-Python-2.7.8.eb => cutadapt-1.5-intel-2014b-Python-2.7.8.eb} (100%) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb similarity index 100% rename from easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb rename to easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb -- GitLab From 955ec3e9a236d4fc3fd0687ea16ccc79d1e8eb6e Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 10:19:56 +0200 Subject: [PATCH 344/992] fixed remarks --- .../c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb | 2 +- .../c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb index 9be9435a32..8a431e4a45 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb index 1c463c28a1..737e7e93bb 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -29,9 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt',], + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } moduleclass = 'bio' - -- GitLab From 9bb645985ef91f8119d1f8e860e01050f8c4a3c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 11:14:44 +0200 Subject: [PATCH 345/992] add easyconfig for networkx --- ...networkx-1.9.1-intel-2015a-Python-2.7.9.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f6ae1e74b7 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.9.1' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +moduleclass = 'tools' -- GitLab From 21ae64206431c783930c3a153769ea138f950518 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 15:23:36 +0200 Subject: [PATCH 346/992] add easyconfig for scikit-learn v0.16.1 --- ...t-learn-0.16.1-intel-2015a-Python-2.7.9.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..8b997036dd --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.4.3', versionsuffix), +] + +options = {'modulename': "sklearn"} + +moduleclass = 'data' -- GitLab From 76564b498593ea34b852f40d935011b16ef293ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 22:06:49 +0200 Subject: [PATCH 347/992] list tcsh as build dep in WRF built with CrayGNU, rather than providing it as a build dep --- .../easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb index 3806e63de1..aecb28f087 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -16,7 +16,10 @@ source_urls = [ ] # csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] +# tcsh provided via EasyBuild may cause build to hang (in interactive configure?) +# ncurses related issue? rebuild tcsh without EB-provided ncurses? +#builddependencies = [('tcsh', '6.18.01')] +osdependencies = ['tcsh'] dependencies = [ ('JasPer', '1.900.1'), -- GitLab From 560459d37056e8ffa48567f623a9468356a76944 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 11:20:50 +0100 Subject: [PATCH 348/992] Add Plumed easyconfig --- .../easyconfigs/p/plumed/configure.patch | 39 +++++++++++++++++++ .../p/plumed/plumed-2.0.4-ictce-7.1.2.eb | 34 ++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/plumed/configure.patch create mode 100644 easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb diff --git a/easybuild/easyconfigs/p/plumed/configure.patch b/easybuild/easyconfigs/p/plumed/configure.patch new file mode 100644 index 0000000000..c96081c3a8 --- /dev/null +++ b/easybuild/easyconfigs/p/plumed/configure.patch @@ -0,0 +1,39 @@ +# patch to work around the hideous build system of plumed. We use the values +# EB sets in the build system. +diff -urN plumed-2.0.4.orig/configurations/linux.icc plumed-2.0.4/configurations/linux.icc +--- plumed-2.0.4.orig/configurations/linux.icc 2014-09-15 11:41:47.000000000 +0200 ++++ plumed-2.0.4/configurations/linux.icc 2014-12-01 14:54:42.000000000 +0100 +@@ -2,21 +2,21 @@ + #CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG + +-LIBS=-ldl ++LIBS:=-ldl $(LIBS) +-DYNAMIC_LIBS=-lstdc++ -llapack -lblas ++DYNAMIC_LIBS:=-lstdc++ $(LIBS) $(LIBLAPACK) + DOUBLEPRECISION=-r8 + +-CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) +-CXXFLAGS=-O -fPIC -Wall -wd981,383,1418 +-CFLAGS=-O -fPIC -Wall ++CPPFLAGS:=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(CPPFLAGS) ++CXXFLAGS:=-O -fPIC -Wall -wd981,383,1418 $(CXXFLAGS) ++CFLAGS:=-O -fPIC -Wall $(CFLAGS) + +-LDFLAGS=-rdynamic ++LDFLAGS:=-rdynamic $(LDFLAGS) + SOEXT=so +-LDSO=icc -shared $(CFLAGS) +-LD=icpc +-LDF90=ifort +-CXX=icpc +-CC=icc +-FC=ifort ++LDSO:=$(CC) -shared $(CFLAGS) ++LD:=$(CXX) ++LDF90:=$(F90) ++CXX:=$(CXX) ++CC:=$(CC) ++FC:=$(F77) + + GCCDEP=g++ + diff --git a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb new file mode 100644 index 0000000000..08d824f5cf --- /dev/null +++ b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb @@ -0,0 +1,34 @@ +# This is a quickly made easyconfig, using some dirty tricks... +# Warning: Here be dragons +# by Ward Poelmans + +name = 'plumed' +version = '2.0.4' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which +works together with some of the most popular molecular dynamics engines. Free energy calculations can be +performed as a function of many order parameters with a particular focus on biological problems, using +state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. +The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} + +# Download from http://www.plumed-code.org/get-it, google drive doesn't allow for clean download url +sources = ['plumed-2.0.4.tgz'] + +patches = ['configure.patch'] + +preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " +preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +# should probably happen in a easyblock. This vars needs to be set +modextrapaths = {'PLUMED_KERNEL': 'lib/libplumedKernel.so'} + +moduleclass = 'chem' -- GitLab From 31932b90aee480fc2f376ba3706689c5a03667c6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 12 May 2015 10:11:05 +0200 Subject: [PATCH 349/992] Updated plumed --- .../p/plumed/{configure.patch => configure-2.0.4.patch} | 0 easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb | 5 +++-- 2 files changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/plumed/{configure.patch => configure-2.0.4.patch} (100%) diff --git a/easybuild/easyconfigs/p/plumed/configure.patch b/easybuild/easyconfigs/p/plumed/configure-2.0.4.patch similarity index 100% rename from easybuild/easyconfigs/p/plumed/configure.patch rename to easybuild/easyconfigs/p/plumed/configure-2.0.4.patch diff --git a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb index 08d824f5cf..b146ba0970 100644 --- a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb @@ -16,9 +16,10 @@ The software, written in C++, can be easily interfaced with both fortran and C/C toolchain = {'name': 'ictce', 'version': '7.1.2'} # Download from http://www.plumed-code.org/get-it, google drive doesn't allow for clean download url -sources = ['plumed-2.0.4.tgz'] +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v2.0.4.tar.gz'] -patches = ['configure.patch'] +patches = ['configure-%(version)s.patch'] preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " -- GitLab From 6fece1573017a6442de47ed240629d5ebbce8e67 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 12 May 2015 11:09:44 +0200 Subject: [PATCH 350/992] added easyblock line --- easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb index b146ba0970..3eda065ef1 100644 --- a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb @@ -2,6 +2,8 @@ # Warning: Here be dragons # by Ward Poelmans +easyblock = 'ConfigureMake' + name = 'plumed' version = '2.0.4' -- GitLab From ba29611f7e2ffd4e6bd2232ff367088395e06a57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 11:37:19 +0200 Subject: [PATCH 351/992] add easyconfig for Platanus (binary) --- .../p/Platanus/Platanus-1.2.1-linux-x86_64.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb new file mode 100644 index 0000000000..c7b0660395 --- /dev/null +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -0,0 +1,20 @@ +easyblock = 'Binary' + +name = 'Platanus' +version = '1.2.1' + +homepage = 'http://platanus.bio.titech.ac.jp/' +description = """PLATform for Assembling NUcleotide Sequences""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201'] +sources = ['platanus'] +checksums = ['02cf92847ec704d010a54df293b9c60a'] + +sanity_check_paths = { + 'files': ['platanus'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a66a1e81e0bb6298a540ec3e86b23c8e48785836 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 14:39:33 +0200 Subject: [PATCH 352/992] fix versionsuffix in Platanus easyconfig --- easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb index c7b0660395..2fa31617c3 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -2,6 +2,7 @@ easyblock = 'Binary' name = 'Platanus' version = '1.2.1' +versionsuffix = '-linux-x86_64' homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" -- GitLab From 85fedfc05c73a04c7d63b0bc8bf6f86894cbc518 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 12 May 2015 14:42:47 +0200 Subject: [PATCH 353/992] added python 3.4.3 intel 2015a --- .../p/Python/Python-3.4.3-intel-2015a.eb | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb new file mode 100644 index 0000000000..d0fad95102 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '3.4.3' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] -- GitLab From 6efa2756f2aa3c60766659f37892daa6eddb47c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:03:53 +0200 Subject: [PATCH 354/992] {bio}[intel/2015a] GROMACS 5.0.4 (mt, hybrid) --- .../GROMACS-5.0.4-intel-2015a-hybrid.eb | 42 +++++++++++++++++++ .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..954bb885eb --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb new file mode 100644 index 0000000000..ea167cc786 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From f8578e3c2d71882e2529fc3d359c034c74b2f276 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:06:56 +0200 Subject: [PATCH 355/992] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb | 12 ++---------- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 12 ++---------- 2 files changed, 4 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb index 954bb885eb..0914af5ffd 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb index ea167cc786..f0da8f6053 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), -- GitLab From d6c783a9bb34da485da46ea42fa3887340aa7026 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 21:57:32 +0200 Subject: [PATCH 356/992] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb index 5e23be1026..b6b649c1ec 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '2.8.12'), -- GitLab From 038bff909bf6a5d4d345cd8eb2830ce76a4e1f3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 22:08:13 +0200 Subject: [PATCH 357/992] {bio}[intel/2015a] SaguaroGW --- .../SaguaroGW-20150315-intel-2015a.eb | 31 +++++++++++++++++++ .../SaguaroGW/SaguaroGW_icpc-drop-const.patch | 15 +++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb new file mode 100644 index 0000000000..e922e754a3 --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SaguaroGW' +version = '20150315' + +homepage = 'http://sourceforge.net/projects/saguarogw/' +description = """Saguaro Genome-Wide is a program to detect signatures of selection within populations, strains, + or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in +the genome.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] +# SVN revision r29 +sources = ['%(namelower)s-code-29.zip'] + +patches = ['SaguaroGW_icpc-drop-const.patch'] + +buildopts = 'CPLUSPLUS="$CXX" CC="$CC" OPEN_MP=yes' + +files_to_copy = [(['checkLock', 'CactiCorrelate', 'ChromoPaintCacti', 'ClusterCacti', 'Fasta2HMMFeature', + 'Genotype2HMMFeature', 'FilterCacti', 'HMMClassify', 'HMMTrain', 'HeatMaps', 'LocalTrees', + 'Maf2HMMFeature', 'PullFromFasta', 'Saguaro', 'Saguaro2Phylip', 'VCF2HMMFeature'], 'bin')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch new file mode 100644 index 0000000000..193b028341 --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch @@ -0,0 +1,15 @@ +fix issue with Intel compilers: 'the object has cv-qualifiers that are not compatible with the member function' +author: Kenneth Hoste (Ghent University) +--- /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h.orig 2012-05-16 15:40:12.000000000 +0200 ++++ /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h 2015-05-12 21:54:40.830166431 +0200 +@@ -39,8 +39,8 @@ + string GetName() { return mName; } + string GetDescription() { return mDesc; } + +-friend bool operator< (const commandArg &lhs, +- const commandArg &rhs) ++friend bool operator< (commandArg &lhs, ++ commandArg &rhs) + { + if ( lhs.GetName() < rhs.GetName() ) + return true; -- GitLab From 8a4c1d8fab0c700d8b32108e1d40dd77289a7fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 22:09:26 +0200 Subject: [PATCH 358/992] add MD5sum for SaguaroGW source tarball --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index e922e754a3..994bf42a7a 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -14,6 +14,7 @@ toolchainopts = {'openmp': True} source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] # SVN revision r29 sources = ['%(namelower)s-code-29.zip'] +checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] patches = ['SaguaroGW_icpc-drop-const.patch'] -- GitLab From 4a76afbf4b79f2881f62f7352ee47fcc2e05937d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:33:57 +0100 Subject: [PATCH 360/992] Added Boost for ictce-7.1.2 --- .../Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb new file mode 100644 index 0000000000..d29dcc1cda --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['intellinuxjam_fPIC.patch', 'boost-impi5.patch'] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' -- GitLab From d87786a613a0fc99572a3bd415e11662073f0f0d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:34:59 +0100 Subject: [PATCH 361/992] Added GROMACS 5.0.2 --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb new file mode 100644 index 0000000000..5e23be1026 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.2' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '2.8.12'), + ('libxml2', '2.9.1') +] + +dependencies = [('Boost', '1.55.0', '-Python-2.7.8')] + +moduleclass = 'bio' -- GitLab From 3bce5c75ec8ff9e05fbf0bfda372b549384fb88a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 13:50:39 +0100 Subject: [PATCH 362/992] Added forgotten Boost patch --- .../easyconfigs/b/Boost/boost-impi5.patch | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/boost-impi5.patch diff --git a/easybuild/easyconfigs/b/Boost/boost-impi5.patch b/easybuild/easyconfigs/b/Boost/boost-impi5.patch new file mode 100644 index 0000000000..635da12964 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/boost-impi5.patch @@ -0,0 +1,37 @@ +diff -ur boost_1_55_0.orig/tools/build/v2/tools/mpi.jam boost_1_55_0/tools/build/v2/tools/mpi.jam +--- boost_1_55_0.orig/tools/build/v2/tools/mpi.jam 2012-04-26 23:32:41.000000000 +0200 ++++ boost_1_55_0/tools/build/v2/tools/mpi.jam 2014-09-03 13:45:45.000000000 +0200 +@@ -301,6 +301,16 @@ + } + # OpenMPI and newer versions of LAM-MPI have -showme:compile and + # -showme:link. ++ # Look for MPICH ++ else if [ safe-shell-command "$(command) -show" ] ++ { ++ if $(.debug-configuration) ++ { ++ ECHO "Found MPICH wrapper compiler: $(command)" ; ++ } ++ compile_flags = [ SHELL "$(command) -compile_info" ] ; ++ link_flags = [ SHELL "$(command) -link_info" ] ; ++ } + else if [ safe-shell-command "$(command) -showme:compile" ] && + [ safe-shell-command "$(command) -showme:link" ] + { +@@ -327,16 +337,6 @@ + + result = [ SHELL "$(command) -showme" ] ; + } +- # Look for MPICH +- else if [ safe-shell-command "$(command) -show" ] +- { +- if $(.debug-configuration) +- { +- ECHO "Found MPICH wrapper compiler: $(command)" ; +- } +- compile_flags = [ SHELL "$(command) -compile_info" ] ; +- link_flags = [ SHELL "$(command) -link_info" ] ; +- } + # Sun HPC and Ibm POE + else if [ SHELL "$(command) -v 2>/dev/null" ] + { -- GitLab From 74d3f2808207c46f434390cb41480c539671a58f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 21:57:32 +0200 Subject: [PATCH 363/992] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb index 5e23be1026..b6b649c1ec 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '2.8.12'), -- GitLab From 0c3e0073a7d4fd768f2bbbc753ede3023134ab15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:03:53 +0200 Subject: [PATCH 364/992] {bio}[intel/2015a] GROMACS 5.0.4 (mt, hybrid) --- .../GROMACS-5.0.4-intel-2015a-hybrid.eb | 42 +++++++++++++++++++ .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..954bb885eb --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb new file mode 100644 index 0000000000..ea167cc786 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From 004eb26fd47c91b8d1093bd7be9263b6369629cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:06:56 +0200 Subject: [PATCH 366/992] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb | 12 ++---------- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 12 ++---------- 2 files changed, 4 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb index 954bb885eb..0914af5ffd 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb index ea167cc786..f0da8f6053 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), -- GitLab From 9b3e2a9aef90b62b554a9d2f2428ee41fe239ec2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 09:51:36 +0200 Subject: [PATCH 368/992] drop source_urls that are not guaranteed to work --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index 994bf42a7a..897d3c2fd1 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -11,8 +11,7 @@ the genome.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True} -source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] -# SVN revision r29 +# SVN revision r29, download via http://sourceforge.net/p/saguarogw/code/29/tree/ ('Download Snapshot' link) sources = ['%(namelower)s-code-29.zip'] checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] -- GitLab From 2ec310d55af639adf4b321f603fa8eb459196c24 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 13 May 2015 12:06:31 +0200 Subject: [PATCH 369/992] added python 3.4.1 with intel 2015a toolchain --- .../p/Python/Python-3.4.1-intel-2015a.eb | 103 ++++++++++++++++++ 1 file changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb new file mode 100644 index 0000000000..5769376b00 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -0,0 +1,103 @@ +name = 'Python' +version = '3.4.1' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.1' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-3.4_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# Version updated 08/JULY/2014 +exts_list = [ + ('setuptools', '5.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.3', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s-mkl.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + # tarball has changed upstream, so make sure we get the right version by verifying the checksum + 'checksums': ['ce61468d4c1263e3005737bbed2641f0'], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), +] + +moduleclass = 'lang' -- GitLab From 7c14eff85d3a767241c9f1b6f12a1f02e44b1ac4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:07:27 +0200 Subject: [PATCH 370/992] remove checksum, tarball is generated on the fly and checksum changes --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index 897d3c2fd1..6edbc50c07 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -13,7 +13,6 @@ toolchainopts = {'openmp': True} # SVN revision r29, download via http://sourceforge.net/p/saguarogw/code/29/tree/ ('Download Snapshot' link) sources = ['%(namelower)s-code-29.zip'] -checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] patches = ['SaguaroGW_icpc-drop-const.patch'] -- GitLab From b814e63fbf2f108f325f3abf42fa0fb222f27917 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:14:58 +0200 Subject: [PATCH 371/992] bump extension versions in Python 3.4.3 easyconfig --- .../p/Python/Python-3.4.3-intel-2015a.eb | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index d0fad95102..a2c2596145 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -7,8 +7,8 @@ description = "Python is a programming language that lets you work more quickly toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.9.1' -scipyversion = '0.14.1' +numpyversion = '1.9.2' +scipyversion = '0.15.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev')] # package versions updated Jan 19th 2015 exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') exts_list = [ - ('setuptools', '11.3.1', { + ('setuptools', '15.2', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '6.0.6', { + ('pip', '6.1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), - ('nose', '1.3.4', { + ('nose', '1.3.6', { 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { @@ -56,32 +56,32 @@ exts_list = [ ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), - ('argparse', '1.2.1', { + ('argparse', '1.3.0', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), - ('pbr', '0.10.8', { + ('pbr', '0.11.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.21.2', { + ('Cython', '0.22', { 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('dateutil', '2.4.0', { + ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), - ('deap', '1.0.1', { + ('deap', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), - ('decorator', '3.4.0', { + ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), - ('arff', '2.0.1', { + ('arff', '2.0.2', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), @@ -89,7 +89,7 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), - ('ecdsa', '0.11', { + ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], }), ('paramiko', '1.15.2', { @@ -101,7 +101,7 @@ exts_list = [ ('netifaces', '0.10.4', { 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], }), - ('netaddr', '0.7.13', { + ('netaddr', '0.7.14', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), ] -- GitLab From bfc912718ffdaf2b07149143595abc3c3ad7ade1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:20:45 +0200 Subject: [PATCH 372/992] fix argparse source URL --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index a2c2596145..eca8e6a7b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.11.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], -- GitLab From f4b269542e2687feab55a0a7e8b6a6e91534974b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:25:24 +0200 Subject: [PATCH 373/992] fix deap source template --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index eca8e6a7b9..9e5af7e518 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -76,6 +76,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.2', { -- GitLab From 8196de12be7227bd95d891f4b0229974abae8c3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:41:14 +0200 Subject: [PATCH 374/992] {system}[intel/2015a] OpenSSL 1.0.1m --- .../o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 24 ++ .../OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch | 343 ++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch | 116 ++++++ 3 files changed, 483 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb new file mode 100644 index 0000000000..7665ce0775 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1m' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-%(version)s-fix_parallel_build-1.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch new file mode 100644 index 0000000000..e30b04902b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch @@ -0,0 +1,343 @@ +Fixes build with make -jx, where x is greater than 1 +based on patch for 1.0.1e by Armin K. +diff -ru openssl-1.0.1m.orig/crypto/Makefile openssl-1.0.1m/crypto/Makefile +--- openssl-1.0.1m.orig/crypto/Makefile 2015-03-19 14:38:24.000000000 +0100 ++++ openssl-1.0.1m/crypto/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -85,11 +85,11 @@ + @if [ -z "$(THIS)" ]; then $(MAKE) -f $(TOP)/Makefile reflect THIS=$@; fi + + subdirs: +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +- @target=files; $(RECURSIVE_MAKE) ++ +@target=files; $(RECURSIVE_MAKE) + + links: + @$(PERL) $(TOP)/util/mklink.pl ../include/openssl $(EXHEADER) +@@ -100,7 +100,7 @@ + # lib: $(LIB): are splitted to avoid end-less loop + lib: $(LIB) + @touch lib +-$(LIB): $(LIBOBJ) ++$(LIB): $(LIBOBJ) | subdirs + $(AR) $(LIB) $(LIBOBJ) + [ -z "$(FIPSLIBDIR)" ] || $(AR) $(LIB) $(FIPSLIBDIR)fipscanister.o + $(RANLIB) $(LIB) || echo Never mind. +@@ -111,7 +111,7 @@ + fi + + libs: +- @target=lib; $(RECURSIVE_MAKE) ++ +@target=lib; $(RECURSIVE_MAKE) + + install: + @[ -n "$(INSTALLTOP)" ] # should be set by top Makefile... +@@ -120,7 +120,7 @@ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + lint: + @target=lint; $(RECURSIVE_MAKE) +diff -ru openssl-1.0.1m.orig/engines/Makefile openssl-1.0.1m/engines/Makefile +--- openssl-1.0.1m.orig/engines/Makefile 2015-03-19 14:38:35.000000000 +0100 ++++ openssl-1.0.1m/engines/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -72,7 +72,7 @@ + + all: lib subdirs + +-lib: $(LIBOBJ) ++lib: $(LIBOBJ) | subdirs + @if [ -n "$(SHARED_LIBS)" ]; then \ + set -e; \ + for l in $(LIBNAMES); do \ +@@ -89,7 +89,7 @@ + + subdirs: + echo $(EDIRS) +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +@@ -128,7 +128,7 @@ + mv -f $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx.new $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx ); \ + done; \ + fi +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + tags: + ctags $(SRC) +diff -ru openssl-1.0.1m.orig/Makefile.org openssl-1.0.1m/Makefile.org +--- openssl-1.0.1m.orig/Makefile.org 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Makefile.org 2015-03-31 12:14:56.071786835 +0200 +@@ -273,17 +273,17 @@ + build_libs: build_crypto build_ssl build_engines + + build_crypto: +- @dir=crypto; target=all; $(BUILD_ONE_CMD) +-build_ssl: +- @dir=ssl; target=all; $(BUILD_ONE_CMD) +-build_engines: +- @dir=engines; target=all; $(BUILD_ONE_CMD) +-build_apps: +- @dir=apps; target=all; $(BUILD_ONE_CMD) +-build_tests: +- @dir=test; target=all; $(BUILD_ONE_CMD) +-build_tools: +- @dir=tools; target=all; $(BUILD_ONE_CMD) ++ +@dir=crypto; target=all; $(BUILD_ONE_CMD) ++build_ssl: build_crypto ++ +@dir=ssl; target=all; $(BUILD_ONE_CMD) ++build_engines: build_crypto ++ +@dir=engines; target=all; $(BUILD_ONE_CMD) ++build_apps: build_libs ++ +@dir=apps; target=all; $(BUILD_ONE_CMD) ++build_tests: build_libs ++ +@dir=test; target=all; $(BUILD_ONE_CMD) ++build_tools: build_libs ++ +@dir=tools; target=all; $(BUILD_ONE_CMD) + + all_testapps: build_libs build_testapps + build_testapps: +@@ -538,9 +538,9 @@ + dist_pem_h: + (cd crypto/pem; $(MAKE) -e $(BUILDENV) pem.h; $(MAKE) clean) + +-install: all install_docs install_sw ++install: install_docs install_sw + +-install_sw: ++install_dirs: + @$(PERL) $(TOP)/util/mkdir-p.pl $(INSTALL_PREFIX)$(INSTALLTOP)/bin \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR) \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines \ +@@ -549,12 +549,19 @@ + $(INSTALL_PREFIX)$(OPENSSLDIR)/misc \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/certs \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/private ++ @$(PERL) $(TOP)/util/mkdir-p.pl \ ++ $(INSTALL_PREFIX)$(MANDIR)/man1 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man3 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man5 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man7 ++ ++install_sw: install_dirs + @set -e; headerlist="$(EXHEADER)"; for i in $$headerlist;\ + do \ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @set -e; target=install; $(RECURSIVE_BUILD_CMD) ++ +@set -e; target=install; $(RECURSIVE_BUILD_CMD) + @set -e; liblist="$(LIBS)"; for i in $$liblist ;\ + do \ + if [ -f "$$i" ]; then \ +@@ -634,12 +641,7 @@ + done; \ + done + +-install_docs: +- @$(PERL) $(TOP)/util/mkdir-p.pl \ +- $(INSTALL_PREFIX)$(MANDIR)/man1 \ +- $(INSTALL_PREFIX)$(MANDIR)/man3 \ +- $(INSTALL_PREFIX)$(MANDIR)/man5 \ +- $(INSTALL_PREFIX)$(MANDIR)/man7 ++install_docs: install_dirs + @pod2man="`cd ./util; ./pod2mantest $(PERL)`"; \ + here="`pwd`"; \ + filecase=; \ +diff -ru openssl-1.0.1m.orig/Makefile.shared openssl-1.0.1m/Makefile.shared +--- openssl-1.0.1m.orig/Makefile.shared 2015-01-20 13:33:36.000000000 +0100 ++++ openssl-1.0.1m/Makefile.shared 2015-03-31 12:14:56.071786835 +0200 +@@ -105,6 +105,7 @@ + SHAREDFLAGS="$${SHAREDFLAGS:-$(CFLAGS) $(SHARED_LDFLAGS)}"; \ + LIBPATH=`for x in $$LIBDEPS; do echo $$x; done | sed -e 's/^ *-L//;t' -e d | uniq`; \ + LIBPATH=`echo $$LIBPATH | sed -e 's/ /:/g'`; \ ++ [ -e $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX ] && exit 0; \ + LD_LIBRARY_PATH=$$LIBPATH:$$LD_LIBRARY_PATH \ + $${SHAREDCMD} $${SHAREDFLAGS} \ + -o $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX \ +@@ -122,6 +123,7 @@ + done; \ + fi; \ + if [ -n "$$SHLIB_SOVER" ]; then \ ++ [ -e "$$SHLIB$$SHLIB_SUFFIX" ] || \ + ( $(SET_X); rm -f $$SHLIB$$SHLIB_SUFFIX; \ + ln -s $$prev $$SHLIB$$SHLIB_SUFFIX ); \ + fi; \ +diff -ru openssl-1.0.1m.orig/test/Makefile openssl-1.0.1m/test/Makefile +--- openssl-1.0.1m.orig/test/Makefile 2015-03-19 14:38:37.000000000 +0100 ++++ openssl-1.0.1m/test/Makefile 2015-03-31 12:16:53.684158416 +0200 +@@ -130,7 +130,7 @@ + tags: + ctags $(SRC) + +-tests: exe apps $(TESTS) ++tests: exe $(TESTS) + + apps: + @(cd ..; $(MAKE) DIRS=apps all) +@@ -388,118 +388,118 @@ + link_app.$${shlib_target} + + $(RSATEST)$(EXE_EXT): $(RSATEST).o $(DLIBCRYPTO) +- @target=$(RSATEST); $(BUILD_CMD) ++ +@target=$(RSATEST); $(BUILD_CMD) + + $(BNTEST)$(EXE_EXT): $(BNTEST).o $(DLIBCRYPTO) +- @target=$(BNTEST); $(BUILD_CMD) ++ +@target=$(BNTEST); $(BUILD_CMD) + + $(ECTEST)$(EXE_EXT): $(ECTEST).o $(DLIBCRYPTO) +- @target=$(ECTEST); $(BUILD_CMD) ++ +@target=$(ECTEST); $(BUILD_CMD) + + $(EXPTEST)$(EXE_EXT): $(EXPTEST).o $(DLIBCRYPTO) +- @target=$(EXPTEST); $(BUILD_CMD) ++ +@target=$(EXPTEST); $(BUILD_CMD) + + $(IDEATEST)$(EXE_EXT): $(IDEATEST).o $(DLIBCRYPTO) +- @target=$(IDEATEST); $(BUILD_CMD) ++ +@target=$(IDEATEST); $(BUILD_CMD) + + $(MD2TEST)$(EXE_EXT): $(MD2TEST).o $(DLIBCRYPTO) +- @target=$(MD2TEST); $(BUILD_CMD) ++ +@target=$(MD2TEST); $(BUILD_CMD) + + $(SHATEST)$(EXE_EXT): $(SHATEST).o $(DLIBCRYPTO) +- @target=$(SHATEST); $(BUILD_CMD) ++ +@target=$(SHATEST); $(BUILD_CMD) + + $(SHA1TEST)$(EXE_EXT): $(SHA1TEST).o $(DLIBCRYPTO) +- @target=$(SHA1TEST); $(BUILD_CMD) ++ +@target=$(SHA1TEST); $(BUILD_CMD) + + $(SHA256TEST)$(EXE_EXT): $(SHA256TEST).o $(DLIBCRYPTO) +- @target=$(SHA256TEST); $(BUILD_CMD) ++ +@target=$(SHA256TEST); $(BUILD_CMD) + + $(SHA512TEST)$(EXE_EXT): $(SHA512TEST).o $(DLIBCRYPTO) +- @target=$(SHA512TEST); $(BUILD_CMD) ++ +@target=$(SHA512TEST); $(BUILD_CMD) + + $(RMDTEST)$(EXE_EXT): $(RMDTEST).o $(DLIBCRYPTO) +- @target=$(RMDTEST); $(BUILD_CMD) ++ +@target=$(RMDTEST); $(BUILD_CMD) + + $(MDC2TEST)$(EXE_EXT): $(MDC2TEST).o $(DLIBCRYPTO) +- @target=$(MDC2TEST); $(BUILD_CMD) ++ +@target=$(MDC2TEST); $(BUILD_CMD) + + $(MD4TEST)$(EXE_EXT): $(MD4TEST).o $(DLIBCRYPTO) +- @target=$(MD4TEST); $(BUILD_CMD) ++ +@target=$(MD4TEST); $(BUILD_CMD) + + $(MD5TEST)$(EXE_EXT): $(MD5TEST).o $(DLIBCRYPTO) +- @target=$(MD5TEST); $(BUILD_CMD) ++ +@target=$(MD5TEST); $(BUILD_CMD) + + $(HMACTEST)$(EXE_EXT): $(HMACTEST).o $(DLIBCRYPTO) +- @target=$(HMACTEST); $(BUILD_CMD) ++ +@target=$(HMACTEST); $(BUILD_CMD) + + $(WPTEST)$(EXE_EXT): $(WPTEST).o $(DLIBCRYPTO) +- @target=$(WPTEST); $(BUILD_CMD) ++ +@target=$(WPTEST); $(BUILD_CMD) + + $(RC2TEST)$(EXE_EXT): $(RC2TEST).o $(DLIBCRYPTO) +- @target=$(RC2TEST); $(BUILD_CMD) ++ +@target=$(RC2TEST); $(BUILD_CMD) + + $(BFTEST)$(EXE_EXT): $(BFTEST).o $(DLIBCRYPTO) +- @target=$(BFTEST); $(BUILD_CMD) ++ +@target=$(BFTEST); $(BUILD_CMD) + + $(CASTTEST)$(EXE_EXT): $(CASTTEST).o $(DLIBCRYPTO) +- @target=$(CASTTEST); $(BUILD_CMD) ++ +@target=$(CASTTEST); $(BUILD_CMD) + + $(RC4TEST)$(EXE_EXT): $(RC4TEST).o $(DLIBCRYPTO) +- @target=$(RC4TEST); $(BUILD_CMD) ++ +@target=$(RC4TEST); $(BUILD_CMD) + + $(RC5TEST)$(EXE_EXT): $(RC5TEST).o $(DLIBCRYPTO) +- @target=$(RC5TEST); $(BUILD_CMD) ++ +@target=$(RC5TEST); $(BUILD_CMD) + + $(DESTEST)$(EXE_EXT): $(DESTEST).o $(DLIBCRYPTO) +- @target=$(DESTEST); $(BUILD_CMD) ++ +@target=$(DESTEST); $(BUILD_CMD) + + $(RANDTEST)$(EXE_EXT): $(RANDTEST).o $(DLIBCRYPTO) +- @target=$(RANDTEST); $(BUILD_CMD) ++ +@target=$(RANDTEST); $(BUILD_CMD) + + $(DHTEST)$(EXE_EXT): $(DHTEST).o $(DLIBCRYPTO) +- @target=$(DHTEST); $(BUILD_CMD) ++ +@target=$(DHTEST); $(BUILD_CMD) + + $(DSATEST)$(EXE_EXT): $(DSATEST).o $(DLIBCRYPTO) +- @target=$(DSATEST); $(BUILD_CMD) ++ +@target=$(DSATEST); $(BUILD_CMD) + + $(METHTEST)$(EXE_EXT): $(METHTEST).o $(DLIBCRYPTO) +- @target=$(METHTEST); $(BUILD_CMD) ++ +@target=$(METHTEST); $(BUILD_CMD) + + $(SSLTEST)$(EXE_EXT): $(SSLTEST).o $(DLIBSSL) $(DLIBCRYPTO) +- @target=$(SSLTEST); $(FIPS_BUILD_CMD) ++ +@target=$(SSLTEST); $(FIPS_BUILD_CMD) + + $(ENGINETEST)$(EXE_EXT): $(ENGINETEST).o $(DLIBCRYPTO) +- @target=$(ENGINETEST); $(BUILD_CMD) ++ +@target=$(ENGINETEST); $(BUILD_CMD) + + $(EVPTEST)$(EXE_EXT): $(EVPTEST).o $(DLIBCRYPTO) +- @target=$(EVPTEST); $(BUILD_CMD) ++ +@target=$(EVPTEST); $(BUILD_CMD) + + $(EVPEXTRATEST)$(EXE_EXT): $(EVPEXTRATEST).o $(DLIBCRYPTO) +- @target=$(EVPEXTRATEST); $(BUILD_CMD) ++ +@target=$(EVPEXTRATEST); $(BUILD_CMD) + + $(ECDSATEST)$(EXE_EXT): $(ECDSATEST).o $(DLIBCRYPTO) +- @target=$(ECDSATEST); $(BUILD_CMD) ++ +@target=$(ECDSATEST); $(BUILD_CMD) + + $(ECDHTEST)$(EXE_EXT): $(ECDHTEST).o $(DLIBCRYPTO) +- @target=$(ECDHTEST); $(BUILD_CMD) ++ +@target=$(ECDHTEST); $(BUILD_CMD) + + $(IGETEST)$(EXE_EXT): $(IGETEST).o $(DLIBCRYPTO) +- @target=$(IGETEST); $(BUILD_CMD) ++ +@target=$(IGETEST); $(BUILD_CMD) + + $(JPAKETEST)$(EXE_EXT): $(JPAKETEST).o $(DLIBCRYPTO) +- @target=$(JPAKETEST); $(BUILD_CMD) ++ +@target=$(JPAKETEST); $(BUILD_CMD) + + $(ASN1TEST)$(EXE_EXT): $(ASN1TEST).o $(DLIBCRYPTO) +- @target=$(ASN1TEST); $(BUILD_CMD) ++ +@target=$(ASN1TEST); $(BUILD_CMD) + + $(SRPTEST)$(EXE_EXT): $(SRPTEST).o $(DLIBCRYPTO) +- @target=$(SRPTEST); $(BUILD_CMD) ++ +@target=$(SRPTEST); $(BUILD_CMD) + + $(HEARTBEATTEST)$(EXE_EXT): $(HEARTBEATTEST).o $(DLIBCRYPTO) +- @target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) ++ +@target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) + + $(CONSTTIMETEST)$(EXE_EXT): $(CONSTTIMETEST).o +- @target=$(CONSTTIMETEST) $(BUILD_CMD) ++ +@target=$(CONSTTIMETEST) $(BUILD_CMD) + + #$(AESTEST).o: $(AESTEST).c + # $(CC) -c $(CFLAGS) -DINTERMEDIATE_VALUE_KAT -DTRACE_KAT_MCT $(AESTEST).c diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch new file mode 100644 index 0000000000..16ab3306c7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch @@ -0,0 +1,116 @@ +based on http://openssl.6102.n7.nabble.com/Compiling-OpenSSL-with-icc-td42304.html (http://cvs.openssl.org/chngview?cn=23036) +diff -ru openssl-1.0.1m.orig/Configure openssl-1.0.1m/Configure +--- openssl-1.0.1m.orig/Configure 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Configure 2015-03-31 12:50:44.965133568 +0200 +@@ -351,7 +351,7 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-O3 -Wall::-D_REENTRANT::-ldl:BN_LLONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${armv4_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + #### IA-32 targets... +-"linux-ia32-icc", "icc:-DL_ENDIAN -O2 -no_cpprt::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia32-icc", "icc:-DL_ENDIAN -O2::-D_REENTRANT::-ldl -no_cpprt:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-elf", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -Wall::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-aout", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### +@@ -359,8 +359,9 @@ + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ia64-ecc","ecc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", ++"linux-x86_64-icc", "icc:-DL_ENDIAN -DTERMIO -O2::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux64-s390x", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1416,6 +1417,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1423,13 +1425,18 @@ + } + if ($iccver>=9) + { +- $cflags.=" -i-static"; +- $cflags=~s/\-no_cpprt/-no-cpprt/; ++ $lflags.=" -i-static"; ++ $lflags=~s/\-no_cpprt/-no-cpprt/; + } + if ($iccver>=10) + { +- $cflags=~s/\-i\-static/-static-intel/; ++ $lflags=~s/\-i\-static/-static-intel/; + } ++ if ($iccver>=11) ++ { ++ $cflags.=" -no-intel-extensions"; # disable Cilk ++ $lflags=~s/\-no\-cpprt/-no-cxxlib/; ++ } + } + + # Unlike other OSes (like Solaris, Linux, Tru64, IRIX) BSD run-time +diff -ru openssl-1.0.1m.orig/crypto/aes/aes_x86core.c openssl-1.0.1m/crypto/aes/aes_x86core.c +--- openssl-1.0.1m.orig/crypto/aes/aes_x86core.c 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/aes/aes_x86core.c 2015-03-31 12:28:27.768182812 +0200 +@@ -89,8 +89,10 @@ + #endif + + #undef ROTATE +-#if defined(_MSC_VER) || defined(__ICC) ++#if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++#elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/des/des_locl.h openssl-1.0.1m/crypto/des/des_locl.h +--- openssl-1.0.1m.orig/crypto/des/des_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/des/des_locl.h 2015-03-31 12:52:29.287245531 +0200 +@@ -162,8 +162,10 @@ + } \ + } + +-# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE(a,n) (_lrotr(a,n)) ++#elif defined(__ICC) ++#define ROTATE(a,n) (_rotr(a,n)) + # elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/md32_common.h openssl-1.0.1m/crypto/md32_common.h +--- openssl-1.0.1m.orig/crypto/md32_common.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/md32_common.h 2015-03-31 12:53:03.737932332 +0200 +@@ -142,8 +142,10 @@ + */ + #undef ROTATE + #ifndef PEDANTIC +-# if defined(_MSC_VER) || defined(__ICC) ++# if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++# elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + # elif defined(__MWERKS__) + # if defined(__POWERPC__) + # define ROTATE(a,n) __rlwinm(a,n,0,31) +diff -ru openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h openssl-1.0.1m/crypto/rc5/rc5_locl.h +--- openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/rc5/rc5_locl.h 2015-03-31 12:51:52.976509433 +0200 +@@ -146,9 +146,12 @@ + *((c)++)=(unsigned char)(((l)>> 8L)&0xff), \ + *((c)++)=(unsigned char)(((l) )&0xff)) + +-#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE_l32(a,n) _lrotl(a,n) + # define ROTATE_r32(a,n) _lrotr(a,n) ++#elif defined(__ICC) ++#define ROTATE_l32(a,n) _rotl(a,n) ++#define ROTATE_r32(a,n) _rotr(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE_l32(a,n) ({ register unsigned int ret; \ -- GitLab From ac878e9b4e53948f8642c68c4ee0690edf7be387 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 15:13:04 +0200 Subject: [PATCH 375/992] fix OpenSSL 1.0.1m patch name --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb index 7665ce0775..a127a7e7bb 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-%(version)s-fix_parallel_build-1.patch', + 'OpenSSL-%(version)s_fix-parallel.patch', ] dependencies = [('zlib', '1.2.8')] -- GitLab From e53a0c251081b0103aaa3eb3fb9d1172ae02bd2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 16:21:04 +0200 Subject: [PATCH 376/992] include patch for deap extension in Python 3.4.3 easyconfig --- .../p/Python/Python-3.4.3-intel-2015a.eb | 1 + .../easyconfigs/p/Python/deap-1.0.2_no-README.patch | 13 +++++++++++++ 2 files changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 9e5af7e518..c1fd1209b8 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -78,6 +78,7 @@ exts_list = [ ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': ['deap-1.0.2_no-README.patch'], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch new file mode 100644 index 0000000000..b88bba0d0c --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch @@ -0,0 +1,13 @@ +README.md is not included in tarball, so comment out long description +author: Kenneth Hoste (Ghent University) +--- deap-1.0.2/setup.py.orig 2015-05-13 15:58:21.188127136 +0200 ++++ deap-1.0.2/setup.py 2015-05-13 15:58:30.288556411 +0200 +@@ -19,7 +19,7 @@ + setup(name='deap', + version=deap.__revision__, + description='Distributed Evolutionary Algorithms in Python', +- long_description=read_md('README.md'), ++ #long_description=read_md('README.md'), + author='deap Development Team', + author_email='deap-users@googlegroups.com', + url='https://www.github.com/deap', -- GitLab From 556e7f32fa5f0ac4a159e48a342d7cfa4dee91cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 May 2015 09:19:11 +0200 Subject: [PATCH 377/992] bump subversion for deap extension, drop unnecessary patch --- .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +-- .../easyconfigs/p/Python/deap-1.0.2_no-README.patch | 13 ------------- 2 files changed, 1 insertion(+), 15 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index c1fd1209b8..3265a5bd15 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -76,9 +76,8 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { - 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - 'patches': ['deap-1.0.2_no-README.patch'], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch deleted file mode 100644 index b88bba0d0c..0000000000 --- a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch +++ /dev/null @@ -1,13 +0,0 @@ -README.md is not included in tarball, so comment out long description -author: Kenneth Hoste (Ghent University) ---- deap-1.0.2/setup.py.orig 2015-05-13 15:58:21.188127136 +0200 -+++ deap-1.0.2/setup.py 2015-05-13 15:58:30.288556411 +0200 -@@ -19,7 +19,7 @@ - setup(name='deap', - version=deap.__revision__, - description='Distributed Evolutionary Algorithms in Python', -- long_description=read_md('README.md'), -+ #long_description=read_md('README.md'), - author='deap Development Team', - author_email='deap-users@googlegroups.com', - url='https://www.github.com/deap', -- GitLab From f1c2d8e210f7bf638900d83e5e610f97245434f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 10:13:15 +0200 Subject: [PATCH 378/992] add version 5.2.40 of Cray toolchains + HPL as test case --- .../easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb | 16 ++++++++++++++ .../easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb | 16 ++++++++++++++ .../c/CrayIntel/CrayIntel-5.2.40.eb | 16 ++++++++++++++ .../h/HPL/HPL-2.1-CrayCCE-5.2.40.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayGNU-5.2.40.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-5.2.40.eb | 18 +++++++++++++++ 6 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb new file mode 100644 index 0000000000..b31f4b3a23 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..dbbbbbd303 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb new file mode 100644 index 0000000000..5937accfe4 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb new file mode 100644 index 0000000000..b91a1eb499 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..dcfcc5ca6e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb new file mode 100644 index 0000000000..8a33b68ad9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '5.2.40'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From f92c4e0cc27bb4f4f910ef6e85ffa1396cff06ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 13:36:11 +0200 Subject: [PATCH 379/992] bump version to v2.1.x --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 5b55ee3e55..e89248dca4 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.1.0' +VERSION = '2.1.1dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 08bfd4bc0cd77f1ea1c4f126925c0b5fc725e4ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:18:35 +0200 Subject: [PATCH 380/992] add easyconfig file for EasyBuild v2.1.0 --- .../e/EasyBuild/EasyBuild-2.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb new file mode 100644 index 0000000000..d753a18457 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = "2.1.0" + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/v/vsc-base/', + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.0.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 8eb13ee04f0d3faab28cffe163d3fd83db885d60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:19:52 +0200 Subject: [PATCH 381/992] style fix --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index d753a18457..b11b8ff6c1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' -version = "2.1.0" +version = '2.1.0' homepage = 'http://hpcugent.github.com/easybuild/' description = """EasyBuild is a software build and installation framework -- GitLab From 55bd896831aea6ec4fdef337370fe3ee8c3dc0ed Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 May 2015 18:36:05 +0200 Subject: [PATCH 382/992] Boost 1.58 for intel/2015a --- .../Boost-1.58.0-intel-2015a-Python-2.7.9.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..a209577bba --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From c4571e54605eba98ff436db0a762a773dc23a8e9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 May 2015 18:37:17 +0200 Subject: [PATCH 383/992] Boost 1.58.0 for foss/2015a --- .../Boost-1.58.0-foss-2015a-Python-2.7.9.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..bbef8b760b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 3de5c8412dd0472f36a779f9e0651f057d8863e4 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Tue, 5 May 2015 16:00:36 +0200 Subject: [PATCH 384/992] Adding the easyconfigs for ictce-7.3.5 --- easybuild/easyconfigs/i/icc/icc-2015.3.187.eb | 17 ++++++++++++++ .../i/iccifort/iccifort-2015.3.187.eb | 16 ++++++++++++++ easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb | 21 ++++++++++++++++++ .../easyconfigs/i/ifort/ifort-2015.3.187.eb | 17 ++++++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb | 18 +++++++++++++++ .../i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb | 22 +++++++++++++++++++ .../impi-5.0.3.048-iccifort-2015.3.187.eb | 19 ++++++++++++++++ 7 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/i/icc/icc-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb new file mode 100644 index 0000000000..55dec91be5 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'icc' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_ccompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb new file mode 100644 index 0000000000..8387432380 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb @@ -0,0 +1,16 @@ +easyblock = "Toolchain" + +name = 'iccifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version), + ('ifort', version), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb new file mode 100644 index 0000000000..6190ed2906 --- /dev/null +++ b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'ictce' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '3.187' +compver = '2015.%s' % suff + +dependencies = [ # version/released + ('icc', compver), # Apr 13th 2015 + ('ifort', compver), # Apr 13th 2015 + ('impi', '5.0.3.048', '', ('iccifort', compver)), # Feb 10th 2015 + ('imkl', '11.2.%s' % suff, '', ('iimpi', version)), # Apr 13th 2015 +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb new file mode 100644 index 0000000000..8253a3390b --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'ifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_fcompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb new file mode 100644 index 0000000000..b0fe67cb26 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb @@ -0,0 +1,18 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2015.3.187' +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '5.0.3.048', '', ('iccifort', compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb new file mode 100644 index 0000000000..807b5f2004 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.2.3.187' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '7.3.5'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb new file mode 100644 index 0000000000..5e0972d8f3 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '5.0.3.048' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2015.3.187'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' -- GitLab From 38226e59dc0659a6ccc047c7712d0f135eb193e8 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Wed, 6 May 2015 11:31:15 +0200 Subject: [PATCH 385/992] Adding HPL 2.1 with ictce-7.3.5 --- .../easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb new file mode 100644 index 0000000000..55ab924d7d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From e59e7fca0b6840ae516121c9eaa8d11669239568 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Aug 2014 13:46:16 +0200 Subject: [PATCH 386/992] added new cutadapt for intel --- .../cutadapt-1.5-intel2014b-Python-2.7.8.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..9be9435a32 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.5' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://pypi.python.org/packages/source/c/cutadapt/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From dad3b10a50135f61257f379827de38173e6d5fe6 Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 09:42:44 +0200 Subject: [PATCH 387/992] added even newer cutadapt --- ...cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..1c463c28a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.8.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt',], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From 380614ad77ca07f62bb9f5911deb4688f0f18d51 Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 09:56:11 +0200 Subject: [PATCH 388/992] fixed filename --- ...b-Python-2.7.8.eb => cutadapt-1.5-intel-2014b-Python-2.7.8.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/cutadapt/{cutadapt-1.5-intel2014b-Python-2.7.8.eb => cutadapt-1.5-intel-2014b-Python-2.7.8.eb} (100%) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb similarity index 100% rename from easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb rename to easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb -- GitLab From cb0e0011875100a86535fd58d74ce3267a94a5e2 Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 10:19:56 +0200 Subject: [PATCH 389/992] fixed remarks --- .../c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb | 2 +- .../c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb index 9be9435a32..8a431e4a45 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb index 1c463c28a1..737e7e93bb 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -29,9 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt',], + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } moduleclass = 'bio' - -- GitLab From 3336fa693a4dfcb0c6b4600380bc025b6f4df6d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 11:14:44 +0200 Subject: [PATCH 390/992] add easyconfig for networkx --- ...networkx-1.9.1-intel-2015a-Python-2.7.9.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f6ae1e74b7 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.9.1' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +moduleclass = 'tools' -- GitLab From 8ce753e79e359f691d042787927bd5577cd1ae12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 15:23:36 +0200 Subject: [PATCH 391/992] add easyconfig for scikit-learn v0.16.1 --- ...t-learn-0.16.1-intel-2015a-Python-2.7.9.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..8b997036dd --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.4.3', versionsuffix), +] + +options = {'modulename': "sklearn"} + +moduleclass = 'data' -- GitLab From 93ce24c124f1004bc7bdb8efd5c8ee30afa64cc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 11:37:19 +0200 Subject: [PATCH 392/992] add easyconfig for Platanus (binary) --- .../p/Platanus/Platanus-1.2.1-linux-x86_64.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb new file mode 100644 index 0000000000..c7b0660395 --- /dev/null +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -0,0 +1,20 @@ +easyblock = 'Binary' + +name = 'Platanus' +version = '1.2.1' + +homepage = 'http://platanus.bio.titech.ac.jp/' +description = """PLATform for Assembling NUcleotide Sequences""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201'] +sources = ['platanus'] +checksums = ['02cf92847ec704d010a54df293b9c60a'] + +sanity_check_paths = { + 'files': ['platanus'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6980c64b72428c6e0adca021a9fbc6185b418473 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 14:39:33 +0200 Subject: [PATCH 393/992] fix versionsuffix in Platanus easyconfig --- easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb index c7b0660395..2fa31617c3 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -2,6 +2,7 @@ easyblock = 'Binary' name = 'Platanus' version = '1.2.1' +versionsuffix = '-linux-x86_64' homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" -- GitLab From af2f8f3d2b1c2be50df9504f87821caff900c746 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:33:57 +0100 Subject: [PATCH 394/992] Added Boost for ictce-7.1.2 --- .../Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb new file mode 100644 index 0000000000..d29dcc1cda --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['intellinuxjam_fPIC.patch', 'boost-impi5.patch'] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' -- GitLab From ff98ab8d207b04305ac22c6d72da668fbe523b1b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:34:59 +0100 Subject: [PATCH 395/992] Added GROMACS 5.0.2 --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb new file mode 100644 index 0000000000..5e23be1026 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.2' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '2.8.12'), + ('libxml2', '2.9.1') +] + +dependencies = [('Boost', '1.55.0', '-Python-2.7.8')] + +moduleclass = 'bio' -- GitLab From 516a5a56a437d3ac1344c99558666f8778de53e5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 13:50:39 +0100 Subject: [PATCH 396/992] Added forgotten Boost patch --- .../easyconfigs/b/Boost/boost-impi5.patch | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/boost-impi5.patch diff --git a/easybuild/easyconfigs/b/Boost/boost-impi5.patch b/easybuild/easyconfigs/b/Boost/boost-impi5.patch new file mode 100644 index 0000000000..635da12964 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/boost-impi5.patch @@ -0,0 +1,37 @@ +diff -ur boost_1_55_0.orig/tools/build/v2/tools/mpi.jam boost_1_55_0/tools/build/v2/tools/mpi.jam +--- boost_1_55_0.orig/tools/build/v2/tools/mpi.jam 2012-04-26 23:32:41.000000000 +0200 ++++ boost_1_55_0/tools/build/v2/tools/mpi.jam 2014-09-03 13:45:45.000000000 +0200 +@@ -301,6 +301,16 @@ + } + # OpenMPI and newer versions of LAM-MPI have -showme:compile and + # -showme:link. ++ # Look for MPICH ++ else if [ safe-shell-command "$(command) -show" ] ++ { ++ if $(.debug-configuration) ++ { ++ ECHO "Found MPICH wrapper compiler: $(command)" ; ++ } ++ compile_flags = [ SHELL "$(command) -compile_info" ] ; ++ link_flags = [ SHELL "$(command) -link_info" ] ; ++ } + else if [ safe-shell-command "$(command) -showme:compile" ] && + [ safe-shell-command "$(command) -showme:link" ] + { +@@ -327,16 +337,6 @@ + + result = [ SHELL "$(command) -showme" ] ; + } +- # Look for MPICH +- else if [ safe-shell-command "$(command) -show" ] +- { +- if $(.debug-configuration) +- { +- ECHO "Found MPICH wrapper compiler: $(command)" ; +- } +- compile_flags = [ SHELL "$(command) -compile_info" ] ; +- link_flags = [ SHELL "$(command) -link_info" ] ; +- } + # Sun HPC and Ibm POE + else if [ SHELL "$(command) -v 2>/dev/null" ] + { -- GitLab From 1d203c06dc40e56f65458d55c8d102e1d499b5c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 21:57:32 +0200 Subject: [PATCH 397/992] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb index 5e23be1026..b6b649c1ec 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '2.8.12'), -- GitLab From 58b1fc72996bff6fb05a172f2f57f8c088a78886 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:03:53 +0200 Subject: [PATCH 398/992] {bio}[intel/2015a] GROMACS 5.0.4 (mt, hybrid) --- .../GROMACS-5.0.4-intel-2015a-hybrid.eb | 42 +++++++++++++++++++ .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..954bb885eb --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb new file mode 100644 index 0000000000..ea167cc786 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From b4d9eaf523881e8aef2fd1ae5c39fd9e42d6535d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:06:56 +0200 Subject: [PATCH 399/992] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb | 12 ++---------- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 12 ++---------- 2 files changed, 4 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb index 954bb885eb..0914af5ffd 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb index ea167cc786..f0da8f6053 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), -- GitLab From 36704f8219b0bf683665b5f2d33eb3c0a2b28424 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 22:08:13 +0200 Subject: [PATCH 400/992] {bio}[intel/2015a] SaguaroGW --- .../SaguaroGW-20150315-intel-2015a.eb | 31 +++++++++++++++++++ .../SaguaroGW/SaguaroGW_icpc-drop-const.patch | 15 +++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb new file mode 100644 index 0000000000..e922e754a3 --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SaguaroGW' +version = '20150315' + +homepage = 'http://sourceforge.net/projects/saguarogw/' +description = """Saguaro Genome-Wide is a program to detect signatures of selection within populations, strains, + or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in +the genome.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] +# SVN revision r29 +sources = ['%(namelower)s-code-29.zip'] + +patches = ['SaguaroGW_icpc-drop-const.patch'] + +buildopts = 'CPLUSPLUS="$CXX" CC="$CC" OPEN_MP=yes' + +files_to_copy = [(['checkLock', 'CactiCorrelate', 'ChromoPaintCacti', 'ClusterCacti', 'Fasta2HMMFeature', + 'Genotype2HMMFeature', 'FilterCacti', 'HMMClassify', 'HMMTrain', 'HeatMaps', 'LocalTrees', + 'Maf2HMMFeature', 'PullFromFasta', 'Saguaro', 'Saguaro2Phylip', 'VCF2HMMFeature'], 'bin')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch new file mode 100644 index 0000000000..193b028341 --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch @@ -0,0 +1,15 @@ +fix issue with Intel compilers: 'the object has cv-qualifiers that are not compatible with the member function' +author: Kenneth Hoste (Ghent University) +--- /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h.orig 2012-05-16 15:40:12.000000000 +0200 ++++ /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h 2015-05-12 21:54:40.830166431 +0200 +@@ -39,8 +39,8 @@ + string GetName() { return mName; } + string GetDescription() { return mDesc; } + +-friend bool operator< (const commandArg &lhs, +- const commandArg &rhs) ++friend bool operator< (commandArg &lhs, ++ commandArg &rhs) + { + if ( lhs.GetName() < rhs.GetName() ) + return true; -- GitLab From b6510084eabdbc338561400131cebb659f561810 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 22:09:26 +0200 Subject: [PATCH 401/992] add MD5sum for SaguaroGW source tarball --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index e922e754a3..994bf42a7a 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -14,6 +14,7 @@ toolchainopts = {'openmp': True} source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] # SVN revision r29 sources = ['%(namelower)s-code-29.zip'] +checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] patches = ['SaguaroGW_icpc-drop-const.patch'] -- GitLab From 76089b1bea669044438b59ccc2670e6e4128e8c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 09:51:36 +0200 Subject: [PATCH 402/992] drop source_urls that are not guaranteed to work --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index 994bf42a7a..897d3c2fd1 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -11,8 +11,7 @@ the genome.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True} -source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] -# SVN revision r29 +# SVN revision r29, download via http://sourceforge.net/p/saguarogw/code/29/tree/ ('Download Snapshot' link) sources = ['%(namelower)s-code-29.zip'] checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] -- GitLab From 86dfb7262445cf3398eda3751c7b5d65904d281a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:07:27 +0200 Subject: [PATCH 403/992] remove checksum, tarball is generated on the fly and checksum changes --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index 897d3c2fd1..6edbc50c07 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -13,7 +13,6 @@ toolchainopts = {'openmp': True} # SVN revision r29, download via http://sourceforge.net/p/saguarogw/code/29/tree/ ('Download Snapshot' link) sources = ['%(namelower)s-code-29.zip'] -checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] patches = ['SaguaroGW_icpc-drop-const.patch'] -- GitLab From 8e6841ad5556e8c355ed664c1ff66184e5a71414 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:41:14 +0200 Subject: [PATCH 404/992] {system}[intel/2015a] OpenSSL 1.0.1m --- .../o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 24 ++ .../OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch | 343 ++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch | 116 ++++++ 3 files changed, 483 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb new file mode 100644 index 0000000000..7665ce0775 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1m' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-%(version)s-fix_parallel_build-1.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch new file mode 100644 index 0000000000..e30b04902b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch @@ -0,0 +1,343 @@ +Fixes build with make -jx, where x is greater than 1 +based on patch for 1.0.1e by Armin K. +diff -ru openssl-1.0.1m.orig/crypto/Makefile openssl-1.0.1m/crypto/Makefile +--- openssl-1.0.1m.orig/crypto/Makefile 2015-03-19 14:38:24.000000000 +0100 ++++ openssl-1.0.1m/crypto/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -85,11 +85,11 @@ + @if [ -z "$(THIS)" ]; then $(MAKE) -f $(TOP)/Makefile reflect THIS=$@; fi + + subdirs: +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +- @target=files; $(RECURSIVE_MAKE) ++ +@target=files; $(RECURSIVE_MAKE) + + links: + @$(PERL) $(TOP)/util/mklink.pl ../include/openssl $(EXHEADER) +@@ -100,7 +100,7 @@ + # lib: $(LIB): are splitted to avoid end-less loop + lib: $(LIB) + @touch lib +-$(LIB): $(LIBOBJ) ++$(LIB): $(LIBOBJ) | subdirs + $(AR) $(LIB) $(LIBOBJ) + [ -z "$(FIPSLIBDIR)" ] || $(AR) $(LIB) $(FIPSLIBDIR)fipscanister.o + $(RANLIB) $(LIB) || echo Never mind. +@@ -111,7 +111,7 @@ + fi + + libs: +- @target=lib; $(RECURSIVE_MAKE) ++ +@target=lib; $(RECURSIVE_MAKE) + + install: + @[ -n "$(INSTALLTOP)" ] # should be set by top Makefile... +@@ -120,7 +120,7 @@ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + lint: + @target=lint; $(RECURSIVE_MAKE) +diff -ru openssl-1.0.1m.orig/engines/Makefile openssl-1.0.1m/engines/Makefile +--- openssl-1.0.1m.orig/engines/Makefile 2015-03-19 14:38:35.000000000 +0100 ++++ openssl-1.0.1m/engines/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -72,7 +72,7 @@ + + all: lib subdirs + +-lib: $(LIBOBJ) ++lib: $(LIBOBJ) | subdirs + @if [ -n "$(SHARED_LIBS)" ]; then \ + set -e; \ + for l in $(LIBNAMES); do \ +@@ -89,7 +89,7 @@ + + subdirs: + echo $(EDIRS) +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +@@ -128,7 +128,7 @@ + mv -f $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx.new $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx ); \ + done; \ + fi +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + tags: + ctags $(SRC) +diff -ru openssl-1.0.1m.orig/Makefile.org openssl-1.0.1m/Makefile.org +--- openssl-1.0.1m.orig/Makefile.org 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Makefile.org 2015-03-31 12:14:56.071786835 +0200 +@@ -273,17 +273,17 @@ + build_libs: build_crypto build_ssl build_engines + + build_crypto: +- @dir=crypto; target=all; $(BUILD_ONE_CMD) +-build_ssl: +- @dir=ssl; target=all; $(BUILD_ONE_CMD) +-build_engines: +- @dir=engines; target=all; $(BUILD_ONE_CMD) +-build_apps: +- @dir=apps; target=all; $(BUILD_ONE_CMD) +-build_tests: +- @dir=test; target=all; $(BUILD_ONE_CMD) +-build_tools: +- @dir=tools; target=all; $(BUILD_ONE_CMD) ++ +@dir=crypto; target=all; $(BUILD_ONE_CMD) ++build_ssl: build_crypto ++ +@dir=ssl; target=all; $(BUILD_ONE_CMD) ++build_engines: build_crypto ++ +@dir=engines; target=all; $(BUILD_ONE_CMD) ++build_apps: build_libs ++ +@dir=apps; target=all; $(BUILD_ONE_CMD) ++build_tests: build_libs ++ +@dir=test; target=all; $(BUILD_ONE_CMD) ++build_tools: build_libs ++ +@dir=tools; target=all; $(BUILD_ONE_CMD) + + all_testapps: build_libs build_testapps + build_testapps: +@@ -538,9 +538,9 @@ + dist_pem_h: + (cd crypto/pem; $(MAKE) -e $(BUILDENV) pem.h; $(MAKE) clean) + +-install: all install_docs install_sw ++install: install_docs install_sw + +-install_sw: ++install_dirs: + @$(PERL) $(TOP)/util/mkdir-p.pl $(INSTALL_PREFIX)$(INSTALLTOP)/bin \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR) \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines \ +@@ -549,12 +549,19 @@ + $(INSTALL_PREFIX)$(OPENSSLDIR)/misc \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/certs \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/private ++ @$(PERL) $(TOP)/util/mkdir-p.pl \ ++ $(INSTALL_PREFIX)$(MANDIR)/man1 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man3 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man5 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man7 ++ ++install_sw: install_dirs + @set -e; headerlist="$(EXHEADER)"; for i in $$headerlist;\ + do \ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @set -e; target=install; $(RECURSIVE_BUILD_CMD) ++ +@set -e; target=install; $(RECURSIVE_BUILD_CMD) + @set -e; liblist="$(LIBS)"; for i in $$liblist ;\ + do \ + if [ -f "$$i" ]; then \ +@@ -634,12 +641,7 @@ + done; \ + done + +-install_docs: +- @$(PERL) $(TOP)/util/mkdir-p.pl \ +- $(INSTALL_PREFIX)$(MANDIR)/man1 \ +- $(INSTALL_PREFIX)$(MANDIR)/man3 \ +- $(INSTALL_PREFIX)$(MANDIR)/man5 \ +- $(INSTALL_PREFIX)$(MANDIR)/man7 ++install_docs: install_dirs + @pod2man="`cd ./util; ./pod2mantest $(PERL)`"; \ + here="`pwd`"; \ + filecase=; \ +diff -ru openssl-1.0.1m.orig/Makefile.shared openssl-1.0.1m/Makefile.shared +--- openssl-1.0.1m.orig/Makefile.shared 2015-01-20 13:33:36.000000000 +0100 ++++ openssl-1.0.1m/Makefile.shared 2015-03-31 12:14:56.071786835 +0200 +@@ -105,6 +105,7 @@ + SHAREDFLAGS="$${SHAREDFLAGS:-$(CFLAGS) $(SHARED_LDFLAGS)}"; \ + LIBPATH=`for x in $$LIBDEPS; do echo $$x; done | sed -e 's/^ *-L//;t' -e d | uniq`; \ + LIBPATH=`echo $$LIBPATH | sed -e 's/ /:/g'`; \ ++ [ -e $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX ] && exit 0; \ + LD_LIBRARY_PATH=$$LIBPATH:$$LD_LIBRARY_PATH \ + $${SHAREDCMD} $${SHAREDFLAGS} \ + -o $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX \ +@@ -122,6 +123,7 @@ + done; \ + fi; \ + if [ -n "$$SHLIB_SOVER" ]; then \ ++ [ -e "$$SHLIB$$SHLIB_SUFFIX" ] || \ + ( $(SET_X); rm -f $$SHLIB$$SHLIB_SUFFIX; \ + ln -s $$prev $$SHLIB$$SHLIB_SUFFIX ); \ + fi; \ +diff -ru openssl-1.0.1m.orig/test/Makefile openssl-1.0.1m/test/Makefile +--- openssl-1.0.1m.orig/test/Makefile 2015-03-19 14:38:37.000000000 +0100 ++++ openssl-1.0.1m/test/Makefile 2015-03-31 12:16:53.684158416 +0200 +@@ -130,7 +130,7 @@ + tags: + ctags $(SRC) + +-tests: exe apps $(TESTS) ++tests: exe $(TESTS) + + apps: + @(cd ..; $(MAKE) DIRS=apps all) +@@ -388,118 +388,118 @@ + link_app.$${shlib_target} + + $(RSATEST)$(EXE_EXT): $(RSATEST).o $(DLIBCRYPTO) +- @target=$(RSATEST); $(BUILD_CMD) ++ +@target=$(RSATEST); $(BUILD_CMD) + + $(BNTEST)$(EXE_EXT): $(BNTEST).o $(DLIBCRYPTO) +- @target=$(BNTEST); $(BUILD_CMD) ++ +@target=$(BNTEST); $(BUILD_CMD) + + $(ECTEST)$(EXE_EXT): $(ECTEST).o $(DLIBCRYPTO) +- @target=$(ECTEST); $(BUILD_CMD) ++ +@target=$(ECTEST); $(BUILD_CMD) + + $(EXPTEST)$(EXE_EXT): $(EXPTEST).o $(DLIBCRYPTO) +- @target=$(EXPTEST); $(BUILD_CMD) ++ +@target=$(EXPTEST); $(BUILD_CMD) + + $(IDEATEST)$(EXE_EXT): $(IDEATEST).o $(DLIBCRYPTO) +- @target=$(IDEATEST); $(BUILD_CMD) ++ +@target=$(IDEATEST); $(BUILD_CMD) + + $(MD2TEST)$(EXE_EXT): $(MD2TEST).o $(DLIBCRYPTO) +- @target=$(MD2TEST); $(BUILD_CMD) ++ +@target=$(MD2TEST); $(BUILD_CMD) + + $(SHATEST)$(EXE_EXT): $(SHATEST).o $(DLIBCRYPTO) +- @target=$(SHATEST); $(BUILD_CMD) ++ +@target=$(SHATEST); $(BUILD_CMD) + + $(SHA1TEST)$(EXE_EXT): $(SHA1TEST).o $(DLIBCRYPTO) +- @target=$(SHA1TEST); $(BUILD_CMD) ++ +@target=$(SHA1TEST); $(BUILD_CMD) + + $(SHA256TEST)$(EXE_EXT): $(SHA256TEST).o $(DLIBCRYPTO) +- @target=$(SHA256TEST); $(BUILD_CMD) ++ +@target=$(SHA256TEST); $(BUILD_CMD) + + $(SHA512TEST)$(EXE_EXT): $(SHA512TEST).o $(DLIBCRYPTO) +- @target=$(SHA512TEST); $(BUILD_CMD) ++ +@target=$(SHA512TEST); $(BUILD_CMD) + + $(RMDTEST)$(EXE_EXT): $(RMDTEST).o $(DLIBCRYPTO) +- @target=$(RMDTEST); $(BUILD_CMD) ++ +@target=$(RMDTEST); $(BUILD_CMD) + + $(MDC2TEST)$(EXE_EXT): $(MDC2TEST).o $(DLIBCRYPTO) +- @target=$(MDC2TEST); $(BUILD_CMD) ++ +@target=$(MDC2TEST); $(BUILD_CMD) + + $(MD4TEST)$(EXE_EXT): $(MD4TEST).o $(DLIBCRYPTO) +- @target=$(MD4TEST); $(BUILD_CMD) ++ +@target=$(MD4TEST); $(BUILD_CMD) + + $(MD5TEST)$(EXE_EXT): $(MD5TEST).o $(DLIBCRYPTO) +- @target=$(MD5TEST); $(BUILD_CMD) ++ +@target=$(MD5TEST); $(BUILD_CMD) + + $(HMACTEST)$(EXE_EXT): $(HMACTEST).o $(DLIBCRYPTO) +- @target=$(HMACTEST); $(BUILD_CMD) ++ +@target=$(HMACTEST); $(BUILD_CMD) + + $(WPTEST)$(EXE_EXT): $(WPTEST).o $(DLIBCRYPTO) +- @target=$(WPTEST); $(BUILD_CMD) ++ +@target=$(WPTEST); $(BUILD_CMD) + + $(RC2TEST)$(EXE_EXT): $(RC2TEST).o $(DLIBCRYPTO) +- @target=$(RC2TEST); $(BUILD_CMD) ++ +@target=$(RC2TEST); $(BUILD_CMD) + + $(BFTEST)$(EXE_EXT): $(BFTEST).o $(DLIBCRYPTO) +- @target=$(BFTEST); $(BUILD_CMD) ++ +@target=$(BFTEST); $(BUILD_CMD) + + $(CASTTEST)$(EXE_EXT): $(CASTTEST).o $(DLIBCRYPTO) +- @target=$(CASTTEST); $(BUILD_CMD) ++ +@target=$(CASTTEST); $(BUILD_CMD) + + $(RC4TEST)$(EXE_EXT): $(RC4TEST).o $(DLIBCRYPTO) +- @target=$(RC4TEST); $(BUILD_CMD) ++ +@target=$(RC4TEST); $(BUILD_CMD) + + $(RC5TEST)$(EXE_EXT): $(RC5TEST).o $(DLIBCRYPTO) +- @target=$(RC5TEST); $(BUILD_CMD) ++ +@target=$(RC5TEST); $(BUILD_CMD) + + $(DESTEST)$(EXE_EXT): $(DESTEST).o $(DLIBCRYPTO) +- @target=$(DESTEST); $(BUILD_CMD) ++ +@target=$(DESTEST); $(BUILD_CMD) + + $(RANDTEST)$(EXE_EXT): $(RANDTEST).o $(DLIBCRYPTO) +- @target=$(RANDTEST); $(BUILD_CMD) ++ +@target=$(RANDTEST); $(BUILD_CMD) + + $(DHTEST)$(EXE_EXT): $(DHTEST).o $(DLIBCRYPTO) +- @target=$(DHTEST); $(BUILD_CMD) ++ +@target=$(DHTEST); $(BUILD_CMD) + + $(DSATEST)$(EXE_EXT): $(DSATEST).o $(DLIBCRYPTO) +- @target=$(DSATEST); $(BUILD_CMD) ++ +@target=$(DSATEST); $(BUILD_CMD) + + $(METHTEST)$(EXE_EXT): $(METHTEST).o $(DLIBCRYPTO) +- @target=$(METHTEST); $(BUILD_CMD) ++ +@target=$(METHTEST); $(BUILD_CMD) + + $(SSLTEST)$(EXE_EXT): $(SSLTEST).o $(DLIBSSL) $(DLIBCRYPTO) +- @target=$(SSLTEST); $(FIPS_BUILD_CMD) ++ +@target=$(SSLTEST); $(FIPS_BUILD_CMD) + + $(ENGINETEST)$(EXE_EXT): $(ENGINETEST).o $(DLIBCRYPTO) +- @target=$(ENGINETEST); $(BUILD_CMD) ++ +@target=$(ENGINETEST); $(BUILD_CMD) + + $(EVPTEST)$(EXE_EXT): $(EVPTEST).o $(DLIBCRYPTO) +- @target=$(EVPTEST); $(BUILD_CMD) ++ +@target=$(EVPTEST); $(BUILD_CMD) + + $(EVPEXTRATEST)$(EXE_EXT): $(EVPEXTRATEST).o $(DLIBCRYPTO) +- @target=$(EVPEXTRATEST); $(BUILD_CMD) ++ +@target=$(EVPEXTRATEST); $(BUILD_CMD) + + $(ECDSATEST)$(EXE_EXT): $(ECDSATEST).o $(DLIBCRYPTO) +- @target=$(ECDSATEST); $(BUILD_CMD) ++ +@target=$(ECDSATEST); $(BUILD_CMD) + + $(ECDHTEST)$(EXE_EXT): $(ECDHTEST).o $(DLIBCRYPTO) +- @target=$(ECDHTEST); $(BUILD_CMD) ++ +@target=$(ECDHTEST); $(BUILD_CMD) + + $(IGETEST)$(EXE_EXT): $(IGETEST).o $(DLIBCRYPTO) +- @target=$(IGETEST); $(BUILD_CMD) ++ +@target=$(IGETEST); $(BUILD_CMD) + + $(JPAKETEST)$(EXE_EXT): $(JPAKETEST).o $(DLIBCRYPTO) +- @target=$(JPAKETEST); $(BUILD_CMD) ++ +@target=$(JPAKETEST); $(BUILD_CMD) + + $(ASN1TEST)$(EXE_EXT): $(ASN1TEST).o $(DLIBCRYPTO) +- @target=$(ASN1TEST); $(BUILD_CMD) ++ +@target=$(ASN1TEST); $(BUILD_CMD) + + $(SRPTEST)$(EXE_EXT): $(SRPTEST).o $(DLIBCRYPTO) +- @target=$(SRPTEST); $(BUILD_CMD) ++ +@target=$(SRPTEST); $(BUILD_CMD) + + $(HEARTBEATTEST)$(EXE_EXT): $(HEARTBEATTEST).o $(DLIBCRYPTO) +- @target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) ++ +@target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) + + $(CONSTTIMETEST)$(EXE_EXT): $(CONSTTIMETEST).o +- @target=$(CONSTTIMETEST) $(BUILD_CMD) ++ +@target=$(CONSTTIMETEST) $(BUILD_CMD) + + #$(AESTEST).o: $(AESTEST).c + # $(CC) -c $(CFLAGS) -DINTERMEDIATE_VALUE_KAT -DTRACE_KAT_MCT $(AESTEST).c diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch new file mode 100644 index 0000000000..16ab3306c7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch @@ -0,0 +1,116 @@ +based on http://openssl.6102.n7.nabble.com/Compiling-OpenSSL-with-icc-td42304.html (http://cvs.openssl.org/chngview?cn=23036) +diff -ru openssl-1.0.1m.orig/Configure openssl-1.0.1m/Configure +--- openssl-1.0.1m.orig/Configure 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Configure 2015-03-31 12:50:44.965133568 +0200 +@@ -351,7 +351,7 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-O3 -Wall::-D_REENTRANT::-ldl:BN_LLONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${armv4_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + #### IA-32 targets... +-"linux-ia32-icc", "icc:-DL_ENDIAN -O2 -no_cpprt::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia32-icc", "icc:-DL_ENDIAN -O2::-D_REENTRANT::-ldl -no_cpprt:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-elf", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -Wall::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-aout", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### +@@ -359,8 +359,9 @@ + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ia64-ecc","ecc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", ++"linux-x86_64-icc", "icc:-DL_ENDIAN -DTERMIO -O2::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux64-s390x", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1416,6 +1417,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1423,13 +1425,18 @@ + } + if ($iccver>=9) + { +- $cflags.=" -i-static"; +- $cflags=~s/\-no_cpprt/-no-cpprt/; ++ $lflags.=" -i-static"; ++ $lflags=~s/\-no_cpprt/-no-cpprt/; + } + if ($iccver>=10) + { +- $cflags=~s/\-i\-static/-static-intel/; ++ $lflags=~s/\-i\-static/-static-intel/; + } ++ if ($iccver>=11) ++ { ++ $cflags.=" -no-intel-extensions"; # disable Cilk ++ $lflags=~s/\-no\-cpprt/-no-cxxlib/; ++ } + } + + # Unlike other OSes (like Solaris, Linux, Tru64, IRIX) BSD run-time +diff -ru openssl-1.0.1m.orig/crypto/aes/aes_x86core.c openssl-1.0.1m/crypto/aes/aes_x86core.c +--- openssl-1.0.1m.orig/crypto/aes/aes_x86core.c 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/aes/aes_x86core.c 2015-03-31 12:28:27.768182812 +0200 +@@ -89,8 +89,10 @@ + #endif + + #undef ROTATE +-#if defined(_MSC_VER) || defined(__ICC) ++#if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++#elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/des/des_locl.h openssl-1.0.1m/crypto/des/des_locl.h +--- openssl-1.0.1m.orig/crypto/des/des_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/des/des_locl.h 2015-03-31 12:52:29.287245531 +0200 +@@ -162,8 +162,10 @@ + } \ + } + +-# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE(a,n) (_lrotr(a,n)) ++#elif defined(__ICC) ++#define ROTATE(a,n) (_rotr(a,n)) + # elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/md32_common.h openssl-1.0.1m/crypto/md32_common.h +--- openssl-1.0.1m.orig/crypto/md32_common.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/md32_common.h 2015-03-31 12:53:03.737932332 +0200 +@@ -142,8 +142,10 @@ + */ + #undef ROTATE + #ifndef PEDANTIC +-# if defined(_MSC_VER) || defined(__ICC) ++# if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++# elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + # elif defined(__MWERKS__) + # if defined(__POWERPC__) + # define ROTATE(a,n) __rlwinm(a,n,0,31) +diff -ru openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h openssl-1.0.1m/crypto/rc5/rc5_locl.h +--- openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/rc5/rc5_locl.h 2015-03-31 12:51:52.976509433 +0200 +@@ -146,9 +146,12 @@ + *((c)++)=(unsigned char)(((l)>> 8L)&0xff), \ + *((c)++)=(unsigned char)(((l) )&0xff)) + +-#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE_l32(a,n) _lrotl(a,n) + # define ROTATE_r32(a,n) _lrotr(a,n) ++#elif defined(__ICC) ++#define ROTATE_l32(a,n) _rotl(a,n) ++#define ROTATE_r32(a,n) _rotr(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE_l32(a,n) ({ register unsigned int ret; \ -- GitLab From b031cab7df4eecc84a831a406496436d757b0e68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 15:13:04 +0200 Subject: [PATCH 405/992] fix OpenSSL 1.0.1m patch name --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb index 7665ce0775..a127a7e7bb 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-%(version)s-fix_parallel_build-1.patch', + 'OpenSSL-%(version)s_fix-parallel.patch', ] dependencies = [('zlib', '1.2.8')] -- GitLab From 2515a635d62a5d85ec1e267dbfbf72bfed64cac4 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 13 May 2015 12:06:31 +0200 Subject: [PATCH 406/992] added python 3.4.1 with intel 2015a toolchain --- .../p/Python/Python-3.4.1-intel-2015a.eb | 103 ++++++++++++++++++ 1 file changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb new file mode 100644 index 0000000000..5769376b00 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -0,0 +1,103 @@ +name = 'Python' +version = '3.4.1' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.1' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-3.4_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# Version updated 08/JULY/2014 +exts_list = [ + ('setuptools', '5.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.3', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s-mkl.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + # tarball has changed upstream, so make sure we get the right version by verifying the checksum + 'checksums': ['ce61468d4c1263e3005737bbed2641f0'], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), +] + +moduleclass = 'lang' -- GitLab From ab0c00b9fdfb4ab34672f873afaadb66266a3697 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 12 May 2015 14:42:47 +0200 Subject: [PATCH 407/992] added python 3.4.3 intel 2015a --- .../p/Python/Python-3.4.3-intel-2015a.eb | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb new file mode 100644 index 0000000000..d0fad95102 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '3.4.3' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] -- GitLab From 7c5a920698c566bf60d7a801d602972c7c9420dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:14:58 +0200 Subject: [PATCH 408/992] bump extension versions in Python 3.4.3 easyconfig --- .../p/Python/Python-3.4.3-intel-2015a.eb | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index d0fad95102..a2c2596145 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -7,8 +7,8 @@ description = "Python is a programming language that lets you work more quickly toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.9.1' -scipyversion = '0.14.1' +numpyversion = '1.9.2' +scipyversion = '0.15.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev')] # package versions updated Jan 19th 2015 exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') exts_list = [ - ('setuptools', '11.3.1', { + ('setuptools', '15.2', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '6.0.6', { + ('pip', '6.1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), - ('nose', '1.3.4', { + ('nose', '1.3.6', { 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { @@ -56,32 +56,32 @@ exts_list = [ ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), - ('argparse', '1.2.1', { + ('argparse', '1.3.0', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), - ('pbr', '0.10.8', { + ('pbr', '0.11.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.21.2', { + ('Cython', '0.22', { 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('dateutil', '2.4.0', { + ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), - ('deap', '1.0.1', { + ('deap', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), - ('decorator', '3.4.0', { + ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), - ('arff', '2.0.1', { + ('arff', '2.0.2', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), @@ -89,7 +89,7 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), - ('ecdsa', '0.11', { + ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], }), ('paramiko', '1.15.2', { @@ -101,7 +101,7 @@ exts_list = [ ('netifaces', '0.10.4', { 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], }), - ('netaddr', '0.7.13', { + ('netaddr', '0.7.14', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), ] -- GitLab From 7e8feed77c7d66b2cbb1d6e639d06e20675752f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:20:45 +0200 Subject: [PATCH 409/992] fix argparse source URL --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index a2c2596145..eca8e6a7b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.11.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], -- GitLab From 709871afa62c5c125a7c6bd46b5af3781d25dbe4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:25:24 +0200 Subject: [PATCH 410/992] fix deap source template --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index eca8e6a7b9..9e5af7e518 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -76,6 +76,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.2', { -- GitLab From 0c3fc06d04290127ce15b3908e009778613dcc24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 16:21:04 +0200 Subject: [PATCH 411/992] include patch for deap extension in Python 3.4.3 easyconfig --- .../p/Python/Python-3.4.3-intel-2015a.eb | 1 + .../easyconfigs/p/Python/deap-1.0.2_no-README.patch | 13 +++++++++++++ 2 files changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 9e5af7e518..c1fd1209b8 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -78,6 +78,7 @@ exts_list = [ ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': ['deap-1.0.2_no-README.patch'], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch new file mode 100644 index 0000000000..b88bba0d0c --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch @@ -0,0 +1,13 @@ +README.md is not included in tarball, so comment out long description +author: Kenneth Hoste (Ghent University) +--- deap-1.0.2/setup.py.orig 2015-05-13 15:58:21.188127136 +0200 ++++ deap-1.0.2/setup.py 2015-05-13 15:58:30.288556411 +0200 +@@ -19,7 +19,7 @@ + setup(name='deap', + version=deap.__revision__, + description='Distributed Evolutionary Algorithms in Python', +- long_description=read_md('README.md'), ++ #long_description=read_md('README.md'), + author='deap Development Team', + author_email='deap-users@googlegroups.com', + url='https://www.github.com/deap', -- GitLab From 59a7685480a80ea6e0493b60d2a9c736a6189a1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 May 2015 09:19:11 +0200 Subject: [PATCH 412/992] bump subversion for deap extension, drop unnecessary patch --- .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +-- .../easyconfigs/p/Python/deap-1.0.2_no-README.patch | 13 ------------- 2 files changed, 1 insertion(+), 15 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index c1fd1209b8..3265a5bd15 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -76,9 +76,8 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { - 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - 'patches': ['deap-1.0.2_no-README.patch'], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch deleted file mode 100644 index b88bba0d0c..0000000000 --- a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch +++ /dev/null @@ -1,13 +0,0 @@ -README.md is not included in tarball, so comment out long description -author: Kenneth Hoste (Ghent University) ---- deap-1.0.2/setup.py.orig 2015-05-13 15:58:21.188127136 +0200 -+++ deap-1.0.2/setup.py 2015-05-13 15:58:30.288556411 +0200 -@@ -19,7 +19,7 @@ - setup(name='deap', - version=deap.__revision__, - description='Distributed Evolutionary Algorithms in Python', -- long_description=read_md('README.md'), -+ #long_description=read_md('README.md'), - author='deap Development Team', - author_email='deap-users@googlegroups.com', - url='https://www.github.com/deap', -- GitLab From 04cb28e3bcf535261ee816ae0144b049ded5bb33 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 4 May 2015 09:49:11 +0200 Subject: [PATCH 413/992] BLAST+ with foss 2015a --- .../BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..37178f8aa5 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = "2.2.30" +versionsuffix = '-Python-2.7.9' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = ['%(name)s-%(version)s_basename-fixes.patch'] + +dependencies = [('Boost', '1.57.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' + -- GitLab From 38d140ef441956f834faef6efa12ef0cb2b843e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 10:13:15 +0200 Subject: [PATCH 414/992] add version 5.2.40 of Cray toolchains + HPL as test case --- .../easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb | 16 ++++++++++++++ .../easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb | 16 ++++++++++++++ .../c/CrayIntel/CrayIntel-5.2.40.eb | 16 ++++++++++++++ .../h/HPL/HPL-2.1-CrayCCE-5.2.40.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayGNU-5.2.40.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-5.2.40.eb | 18 +++++++++++++++ 6 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb new file mode 100644 index 0000000000..b31f4b3a23 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..dbbbbbd303 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb new file mode 100644 index 0000000000..5937accfe4 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb new file mode 100644 index 0000000000..b91a1eb499 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..dcfcc5ca6e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb new file mode 100644 index 0000000000..8a33b68ad9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '5.2.40'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From d5d049057b951e9fa52840ce987377b8d4e0a441 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 May 2015 15:59:13 +0300 Subject: [PATCH 415/992] enable usempi in GROMACS Cray easyconfig, the easyblock enables MPI support on it --- .../easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb index c7618bc1f3..1aa3886405 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb @@ -19,6 +19,7 @@ description = """GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz source_urls = [ -- GitLab From 114232dd6b90b67f9f3bb61d9a032c2b9b5e8780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 14:45:13 +0200 Subject: [PATCH 416/992] only use 'dynamic' toolchain option, not 'shared', in easyconfigs using Cray toolchain --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb index 64defc00e8..23ac2489aa 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -7,7 +7,7 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'shared': True, 'dynamic': True} +toolchainopts = {'pic': True, 'dynamic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb index 5a2850640d..dfcda740ab 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb @@ -7,7 +7,7 @@ homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'shared': True, 'dynamic': True} +toolchainopts = {'pic': True, 'dynamic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb index 6245093966..b62190e55f 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb @@ -21,7 +21,7 @@ description = """Tcsh is an enhanced, but completely compatible version of the B mechanism, job control and a C-like syntax.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'shared': True, 'dynamic': True} +toolchainopts = {'dynamic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [ diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb index 737b571621..f6714bc2c1 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'shared': True} +toolchainopts = {'pic': True, 'dynamic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -- GitLab From a87232564c6f4ac0c48a03d46ed25abc6b6c06f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 15:18:33 +0200 Subject: [PATCH 418/992] clean up comments --- .../easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb index aecb28f087..cfdc17ab69 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -15,11 +15,9 @@ source_urls = [ 'http://www.mmm.ucar.edu/wrf/src/', ] -# csh is used by WRF install scripts -# tcsh provided via EasyBuild may cause build to hang (in interactive configure?) -# ncurses related issue? rebuild tcsh without EB-provided ncurses? -#builddependencies = [('tcsh', '6.18.01')] +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] dependencies = [ ('JasPer', '1.900.1'), -- GitLab From 4dc228d977e87af658704efd36df9d4a30b3aa8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 22:06:49 +0200 Subject: [PATCH 419/992] list tcsh as build dep in WRF built with CrayGNU, rather than providing it as a build dep --- .../easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb index 3806e63de1..aecb28f087 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -16,7 +16,10 @@ source_urls = [ ] # csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] +# tcsh provided via EasyBuild may cause build to hang (in interactive configure?) +# ncurses related issue? rebuild tcsh without EB-provided ncurses? +#builddependencies = [('tcsh', '6.18.01')] +osdependencies = ['tcsh'] dependencies = [ ('JasPer', '1.900.1'), -- GitLab From fca31c50d3a4efc30b2f05a208a70c2eb8dc482a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 15:18:33 +0200 Subject: [PATCH 420/992] clean up comments --- .../easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb index aecb28f087..cfdc17ab69 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -15,11 +15,9 @@ source_urls = [ 'http://www.mmm.ucar.edu/wrf/src/', ] -# csh is used by WRF install scripts -# tcsh provided via EasyBuild may cause build to hang (in interactive configure?) -# ncurses related issue? rebuild tcsh without EB-provided ncurses? -#builddependencies = [('tcsh', '6.18.01')] +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] dependencies = [ ('JasPer', '1.900.1'), -- GitLab From ad84890dd55eb8282003990306ac64c1ad362726 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 17:33:21 +0200 Subject: [PATCH 421/992] add easyconfigs using CrayGNU/5.2.40 toolchain --- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb | 38 +++++++ .../f/flex/flex-2.5.39-CrayGNU-5.2.40.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb | 38 +++++++ .../j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb | 24 ++++ .../libreadline-6.3-CrayGNU-5.2.40.eb | 27 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb | 32 ++++++ .../m/M4/M4-1.4.17-CrayGNU-5.2.40.eb | 23 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 22 ++++ ...numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.2.40-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 107 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.2.40.eb | 23 ++++ ...cipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb | 19 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb | 39 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb | 41 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb | 22 ++++ 20 files changed, 607 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..67832ccafa --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..58489cb68f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..275dc8cada --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..eea0ba5f73 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..470ec059e0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb new file mode 100644 index 0000000000..239ea564c8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..cef32fd43d --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..4f2df44352 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..7264a9260e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..80df7f4320 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..d1ac7167dc --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..af63de1cff --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000..7d81f886bc --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb new file mode 100644 index 0000000000..10c6659238 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..deac7ecaca --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..d98933db4b --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000..adb35688b3 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..171465e133 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb new file mode 100644 index 0000000000..4f97a28683 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..736d7b43ce --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 3fd381b1986243a3ba19d848b98c4246449750e4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 16 May 2015 17:47:47 +0200 Subject: [PATCH 422/992] update binutils to work with dummy --- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 7 ++--- .../easyconfigs/b/binutils/binutils-2.25.eb | 27 +++++++++++++++++++ easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb | 21 +++++++++++++++ 3 files changed, 52 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index e44a4bc4f7..8f92f6c007 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -11,12 +11,13 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'GCC', 'version': '4.9.2'} -dependencies = [ - ('zlib', '1.2.8'), -] +dependencies = [('zlib', '1.2.8')] + +configopts = '--with-sysroot' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb new file mode 100644 index 0000000000..8b1980cd7d --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [('zlib', '1.2.8')] + +configopts = '--with-sysroot' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb new file mode 100644 index 0000000000..50f8b33ec8 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From b7279aff404dced7a2306aeeecf7f96ece221900 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 16 May 2015 17:48:32 +0200 Subject: [PATCH 423/992] Forgotten dependency --- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 8f92f6c007..f91dda00cd 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} dependencies = [('zlib', '1.2.8')] +builddependencies = [('binutils', '2.25', '', True)] + configopts = '--with-sysroot' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', -- GitLab From 19fdbbcd774288f6c51a6336a0f689d350702968 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 16 May 2015 17:49:58 +0200 Subject: [PATCH 424/992] update gcc to use binutils --- easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index cb9f3aa4f2..dd71a77ce5 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' @@ -22,6 +22,8 @@ sources = [ 'mpc-1.0.2.tar.gz', ] +builddependencies = [('binutils', '2.25')] + patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] checksums = [ -- GitLab From cddd0c9e8349e8c14e1285413bd907ab663eb3af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 23:40:29 +0200 Subject: [PATCH 425/992] add easyconfigs using CrayGNU/5.2.25 toolchain --- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb | 38 +++++++ .../f/flex/flex-2.5.39-CrayGNU-5.2.25.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb | 38 +++++++ .../j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb | 24 ++++ .../libreadline-6.3-CrayGNU-5.2.25.eb | 27 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb | 32 ++++++ .../m/M4/M4-1.4.17-CrayGNU-5.2.25.eb | 23 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 22 ++++ ...numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.2.25-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 107 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.2.25.eb | 23 ++++ ...cipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb | 19 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb | 39 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb | 42 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb | 22 ++++ 20 files changed, 608 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..79f11b47fe --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..3f96190606 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..75190be28b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..43baa97a11 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..e9455b96ac --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb new file mode 100644 index 0000000000..4a945e2af8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..606c94876c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..e7bca79f1d --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..6078f8b7e2 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..79002b6ce4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..06f80557f1 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..95c1010bbc --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000..fa04b42299 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb new file mode 100644 index 0000000000..09917d5025 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..adcd0caa18 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..0772f31b94 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000..be06b3e907 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..c678adaf68 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb new file mode 100644 index 0000000000..b4103d924f --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb @@ -0,0 +1,42 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems +osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..17db62ce98 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 977a898d0a0a34f670efb8eae3eb8eb8264462aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 17:33:21 +0200 Subject: [PATCH 426/992] add easyconfigs using CrayGNU/5.2.40 toolchain --- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb | 38 +++++++ .../f/flex/flex-2.5.39-CrayGNU-5.2.40.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb | 38 +++++++ .../j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb | 24 ++++ .../libreadline-6.3-CrayGNU-5.2.40.eb | 27 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb | 32 ++++++ .../m/M4/M4-1.4.17-CrayGNU-5.2.40.eb | 23 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 22 ++++ ...numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.2.40-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 107 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.2.40.eb | 23 ++++ ...cipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb | 19 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb | 39 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb | 41 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb | 22 ++++ 20 files changed, 607 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..67832ccafa --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..58489cb68f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..275dc8cada --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..eea0ba5f73 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..470ec059e0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb new file mode 100644 index 0000000000..239ea564c8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..cef32fd43d --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..4f2df44352 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..7264a9260e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..80df7f4320 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..d1ac7167dc --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..af63de1cff --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000..7d81f886bc --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb new file mode 100644 index 0000000000..10c6659238 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..deac7ecaca --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..d98933db4b --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000..adb35688b3 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..171465e133 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb new file mode 100644 index 0000000000..4f97a28683 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..736d7b43ce --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 181bd951a6fd8505b74c2c275bc581ffe19a9148 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 23:40:29 +0200 Subject: [PATCH 427/992] add easyconfigs using CrayGNU/5.2.25 toolchain --- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb | 38 +++++++ .../f/flex/flex-2.5.39-CrayGNU-5.2.25.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb | 38 +++++++ .../j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb | 24 ++++ .../libreadline-6.3-CrayGNU-5.2.25.eb | 27 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb | 32 ++++++ .../m/M4/M4-1.4.17-CrayGNU-5.2.25.eb | 23 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 22 ++++ ...numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.2.25-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 107 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.2.25.eb | 23 ++++ ...cipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb | 19 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb | 39 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb | 42 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb | 22 ++++ 20 files changed, 608 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..79f11b47fe --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..3f96190606 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..75190be28b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..43baa97a11 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..e9455b96ac --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb new file mode 100644 index 0000000000..4a945e2af8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..606c94876c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..e7bca79f1d --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..6078f8b7e2 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..79002b6ce4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..06f80557f1 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..95c1010bbc --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000..fa04b42299 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb new file mode 100644 index 0000000000..09917d5025 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..adcd0caa18 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..0772f31b94 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000..be06b3e907 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..c678adaf68 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb new file mode 100644 index 0000000000..b4103d924f --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb @@ -0,0 +1,42 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems +osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..17db62ce98 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 2e364489f116e52784d5999acb4ed117fc5b0d5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 12:15:28 +0200 Subject: [PATCH 432/992] bump version to 2.1.1 and update release notes --- RELEASE_NOTES | 14 +++++++++++++- setup.py | 2 +- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index c00535497a..d718187f88 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,21 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,618 easyconfig files, for 608 different software packages, +The latest version of easybuild-easyconfig provides 3,649 easyconfig files, for 611 different software packages, 33 different (compiler) toolchains and 8 software bundles. +v2.1.1 (May 18th 2015) +---------------------- + +bugfix release +- added example easyconfig files for 3 new software packages: + networkx (#1592), Platanus (#1597), SaguaroGW (#1600) +- added new easyconfigs for existing toolchains: ictce/7.3.5, CrayCCE/5.2.40, CrayGNU/5.2.40, CrayIntel/5.2.40 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3 +- various bug fixes, including: + - enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (#1590) + v2.1.0 (April 30th 2015) ------------------------ diff --git a/setup.py b/setup.py index e89248dca4..7111a82776 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.1.1dev' +VERSION = '2.1.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From b4269fd81f4a535ab684aaf158614bc180a8cf7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 16:06:08 +0200 Subject: [PATCH 433/992] include #1595, #1609 in v2.1.1 release notes --- RELEASE_NOTES | 2 ++ 1 file changed, 2 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index d718187f88..8466fcf171 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -17,6 +17,8 @@ bugfix release including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3 - various bug fixes, including: - enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (#1590) + - use system-provided tcsh when building WRF on Cray systems, to avoid hanging build (#1595) + - only use 'dynamic' toolchain option, not 'shared', in easyconfigs using Cray toolchain (#1609) v2.1.0 (April 30th 2015) ------------------------ -- GitLab From 2baae9592738f1fed3fa6e36fdca64d7090910c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 17 May 2015 09:44:45 +0200 Subject: [PATCH 434/992] includ PRs #1610 and #1611 in release notes --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 8466fcf171..4f2bb65a95 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -13,6 +13,7 @@ bugfix release - added example easyconfig files for 3 new software packages: networkx (#1592), Platanus (#1597), SaguaroGW (#1600) - added new easyconfigs for existing toolchains: ictce/7.3.5, CrayCCE/5.2.40, CrayGNU/5.2.40, CrayIntel/5.2.40 +- added easyconfigs using CrayGNU/5.2.25 and CrayGNU/5.2.40 toolchains (#1610, #1611) - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3 - various bug fixes, including: -- GitLab From 24dd63aaae7a34e34d0119be08d217eaf06b7e34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 09:02:48 +0200 Subject: [PATCH 435/992] fix easyconfigs count --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 4f2bb65a95..b593156524 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,649 easyconfig files, for 611 different software packages, +The latest version of easybuild-easyconfig provides 3,689 easyconfig files, for 611 different software packages, 33 different (compiler) toolchains and 8 software bundles. v2.1.1 (May 18th 2015) -- GitLab From a04d50f343f8599e96d1bf8d68f4934cdadf502f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 13:50:25 +0200 Subject: [PATCH 436/992] {bio}[intel/2015a] MrBayes 3.2.5 --- .../m/MrBayes/MrBayes-3.2.5-intel-2015a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb new file mode 100644 index 0000000000..5836ec7f0f --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb @@ -0,0 +1,18 @@ +name = 'MrBayes' +version = '3.2.5' + +homepage = 'http://mrbayes.csit.fsu.edu' +description = "MrBayes is a program for the Bayesian estimation of phylogeny." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%(version)s"] + +dependencies = [ + ('beagle-lib', '20141202'), + ('libreadline', '6.3'), +] + +moduleclass = 'bio' -- GitLab From 2b9145a950cdf0a5a90e027ced75f7130d08b2e7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 18 May 2015 14:10:47 +0200 Subject: [PATCH 437/992] drop zlib dep in foss & gompi --- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 1 - easybuild/easyconfigs/g/gompi/gompi-2015.01.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb index dfce67f25b..9c0f07775d 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -29,7 +29,6 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ comp, - ('zlib', '1.2.8', '', comp), ('binutils', '2.25', '', comp), ('OpenMPI', '1.8.4', '', comp), (blaslib, blasver, blassuff, comp), diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb index e59112cb7f..1dd2af3813 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb @@ -16,7 +16,6 @@ comp = (compname, compver) # compiler toolchain dependencies dependencies = [ comp, - ('zlib', '1.2.8', '', comp), ('binutils', '2.25', '', comp), ('OpenMPI', '1.8.4', '', comp), ] -- GitLab From 15e64083305ccf18fdeb24d6dc700aa5f3f3d327 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 18 May 2015 14:13:14 +0200 Subject: [PATCH 438/992] forgotten toolchains --- easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb | 1 - easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb index f50cd40115..f8cc89cff5 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb @@ -16,7 +16,6 @@ comp = (compname, compver) # compiler toolchain dependencies dependencies = [ comp, - ('zlib', '1.2.8', '', comp), ('binutils', '2.25', '', comp), ('OpenMPI', '1.8.4', '', comp), ] diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb index 0f2aea75a4..feeb6330ff 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb @@ -28,7 +28,6 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # because of toolchain preperation functions dependencies = [ comp, - ('zlib', '1.2.8', '', comp), ('binutils', '2.25', '', comp), ('OpenMPI', '1.8.4', '', comp), (blaslib, blasver, blassuff, comp), -- GitLab From 462c15dfe12a4805d0ef0a4342537242f4b112bb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 18 May 2015 16:10:12 +0200 Subject: [PATCH 439/992] static link with zlib in dummy binutils --- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 8b1980cd7d..e3e98b2548 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -11,7 +11,11 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'dummy', 'version': ''} -dependencies = [('zlib', '1.2.8')] +builddependencies = [('zlib', '1.2.8')] + +# statically link with zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' configopts = '--with-sysroot' -- GitLab From a164a54aacab9104326fb3cd237753ba3e4830ed Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 18 May 2015 16:17:37 +0200 Subject: [PATCH 440/992] clearfy static linking zlib in binutils --- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index e3e98b2548..9a9d28a75d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'dummy', 'version': ''} builddependencies = [('zlib', '1.2.8')] -# statically link with zlib +# statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -- GitLab From 24863a480808fdfde716c66fdb0f88a332155c94 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Mon, 18 May 2015 10:58:05 -0400 Subject: [PATCH 441/992] fixing version in sanity checks --- easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb index ec8aac5c94..7597335a90 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -20,11 +20,12 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] +# Due to the way versioning works now with ruby, the libraries and such are labelled major.minor.0 sanity_check_paths = { 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.%(version_major_minor)s.0', 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] + 'dirs': ['lib/ruby/%(version_major_minor)s.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-%(version_major_minor)s.0'] } configopts = "--disable-install-doc --enable-shared" -- GitLab From ea7acab60f40e453856e5323a005a7256e82b90c Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Mon, 18 May 2015 11:14:18 -0400 Subject: [PATCH 442/992] moving configopts to easyblock and updating other comments per PR comments --- easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb index 7597335a90..d422f5a2f3 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -28,17 +28,12 @@ sanity_check_paths = { 'dirs': ['lib/ruby/%(version_major_minor)s.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-%(version_major_minor)s.0'] } -configopts = "--disable-install-doc --enable-shared" - -moduleclass = 'lang' - -name_tmpl = '%(name)s-%(version)s.gem' ext_options = { 'source_urls': [ 'http://rubygems.org/downloads/', # gem archive ], - 'source_tmpl': name_tmpl, + 'source_tmpl': '%(name)s-%(version)s.gem', } exts_list = [ @@ -51,3 +46,5 @@ exts_list = [ ('clamp', '0.6.4', ext_options), ('fpm', '1.3.3', ext_options), ] + +moduleclass = 'lang' -- GitLab From b97ff1c4e5b44c4ea3f935b1d1ed1fbbcb67e668 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Mon, 18 May 2015 11:16:12 -0400 Subject: [PATCH 443/992] don't bother committing foss version --- .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 33 ------------------- .../r/Ruby/Ruby-2.1.5-intel-2014b.eb | 33 ------------------- 2 files changed, 66 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb delete mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb deleted file mode 100644 index c585ab1d31..0000000000 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb +++ /dev/null @@ -1,33 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for Ruby 2.1: -# ---------------------------------------------------------------------------- -# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Aaron Zauner -# ---------------------------------------------------------------------------- - -name = 'Ruby' -version = '2.1.5' - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] - -sanity_check_paths = { - 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', - 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] -} - -configopts = "--disable-install-doc --enable-shared" - -moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb deleted file mode 100644 index 32eca44aae..0000000000 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb +++ /dev/null @@ -1,33 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for Ruby 2.1: -# ---------------------------------------------------------------------------- -# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Aaron Zauner -# ---------------------------------------------------------------------------- -easyblock = 'ConfigureMake' - -name = 'Ruby' -version = '2.1.5' - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] - -sanity_check_paths = { - 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', - 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] -} - -configopts = "--disable-install-doc --enable-shared" - -moduleclass = 'lang' -- GitLab From d49bb8dfb55e1d67e8d8e192ee1fd1b22b33ea80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 18:32:14 +0200 Subject: [PATCH 444/992] {tools}[dummy] EasyBuild v2.1.1 --- .../e/EasyBuild/EasyBuild-2.1.1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb new file mode 100644 index 0000000000..f6127ef3f7 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.1.1' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/v/vsc-base/', + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.2.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From ff52953b05070a498f1ce059ab60b203fc491505 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 18:44:18 +0200 Subject: [PATCH 445/992] use https source_urls in EasyBuild 2.1.1 easyconfig --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb index f6127ef3f7..632563276e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb @@ -11,10 +11,10 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/v/vsc-base/', - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ -- GitLab From e079d27c019c59900735ddd457de4576d5f864b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 18:59:52 +0200 Subject: [PATCH 446/992] consistently use https for PyPI URLs in homepage/source_urls --- ...Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../Cython-0.16-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../Cython-0.16-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb | 8 ++++---- .../easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb | 8 ++++---- .../Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb | 2 +- ....4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb | 2 +- .../monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb | 2 +- .../PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb | 2 +- .../p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 10 +++++----- .../p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 10 +++++----- .../p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 10 +++++----- .../p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 10 +++++----- .../p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 10 +++++----- .../p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 10 +++++----- .../p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 10 +++++----- .../p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 10 +++++----- .../p/Python/Python-2.7.3-goolf-1.4.10.eb | 10 +++++----- .../p/Python/Python-2.7.3-goolf-1.5.14.eb | 10 +++++----- .../p/Python/Python-2.7.3-ictce-4.0.6.eb | 10 +++++----- .../p/Python/Python-2.7.3-ictce-4.1.13.eb | 10 +++++----- .../p/Python/Python-2.7.3-ictce-5.2.0.eb | 10 +++++----- .../p/Python/Python-2.7.3-ictce-5.3.0.eb | 10 +++++----- .../p/Python/Python-2.7.3-intel-2015a.eb | 10 +++++----- .../p/Python/Python-2.7.3-iomkl-4.6.13.eb | 10 +++++----- .../p/Python/Python-2.7.3-iqacml-3.7.3.eb | 10 +++++----- .../p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 10 +++++----- .../p/Python/Python-2.7.5-goolf-1.4.10.eb | 10 +++++----- .../p/Python/Python-2.7.5-ictce-4.1.13.eb | 10 +++++----- .../p/Python/Python-2.7.5-ictce-5.3.0.eb | 10 +++++----- .../p/Python/Python-2.7.5-ictce-5.5.0.eb | 10 +++++----- .../p/Python/Python-2.7.5-iqacml-3.7.3.eb | 10 +++++----- .../p/Python/Python-2.7.6-goolf-1.4.10.eb | 10 +++++----- .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 10 +++++----- .../p/Python/Python-2.7.6-ictce-5.5.0.eb | 10 +++++----- .../p/Python/Python-2.7.8-foss-2014b.eb | 10 +++++----- .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 14 +++++++------- .../p/Python/Python-2.7.8-ictce-7.1.2.eb | 12 ++++++------ .../p/Python/Python-2.7.8-intel-2014.06.eb | 12 ++++++------ .../p/Python/Python-2.7.8-intel-2014b.eb | 12 ++++++------ .../p/Python/Python-2.7.8-intel-2015a.eb | 12 ++++++------ .../p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 12 ++++++------ .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 12 ++++++------ .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 12 ++++++------ .../p/Python/Python-2.7.9-foss-2015a.eb | 12 ++++++------ .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 12 ++++++------ .../p/Python/Python-2.7.9-intel-2015a.eb | 12 ++++++------ .../p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 6 +++--- .../p/Python/Python-3.2.3-goolf-1.4.10.eb | 6 +++--- .../p/Python/Python-3.2.3-ictce-4.0.6.eb | 6 +++--- .../p/Python/Python-3.2.3-ictce-5.3.0.eb | 6 +++--- .../p/Python/Python-3.3.2-goolf-1.4.10.eb | 6 +++--- .../p/Python/Python-3.3.2-ictce-4.1.13.eb | 6 +++--- .../p/Python/Python-3.3.2-ictce-5.3.0.eb | 6 +++--- .../p/Python/Python-3.4.1-intel-2014b.eb | 12 ++++++------ .../p/Python/Python-3.4.1-intel-2015a.eb | 12 ++++++------ .../p/Python/Python-3.4.3-intel-2015a.eb | 12 ++++++------ .../pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../pandas-0.16.0-intel-2015a-Python-2.7.9.eb | 2 +- ...check-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 ++---- .../paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb | 6 ++---- .../paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb | 6 ++---- .../paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb | 7 ++----- .../paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb | 6 ++---- ...13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb | 2 +- .../pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb | 2 +- ...ools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 4 ++-- .../setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb | 4 ++-- .../setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb | 5 ++--- .../easyconfigs/s/setuptools/setuptools-1.4.2.eb | 4 ++-- .../stemming-1.0-ictce-5.5.0-Python-2.7.6.eb | 2 +- 113 files changed, 377 insertions(+), 389 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 83aec1d936..01ad882b83 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb index 892d56aaa1..fa53744e7c 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb index b81a538f5c..33197474ce 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb index 6e94f41099..5cd50bc1ae 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb index 5d1302c3c1..f2fb277465 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb index ebccd555bb..0e8ac631d0 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.1' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb index 3c845e9845..37ecdfbd48 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.1' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb index 544e217059..6ba8ee3375 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.1' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb index 6d9476ba0f..80955e4cc6 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.2' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb index 375a69f41e..6a13fbccbd 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb index ceb0952d37..1fc508215c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb index 335d94e6fb..aefe4f3461 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb index 22d8fd70bd..aec17460aa 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb index 99d04a46aa..12381b6467 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb index e4ebd91d1b..a8ef6b164a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb index 798cd20488..d2df7f1988 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb index b7092a63e9..345d210d28 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb index f8cd7d18f2..97720876b9 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb index 1b3cf50b1a..0b5ba14c24 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb index 8ceec790c8..0176f2b558 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb index cfc44c499c..3ae286c658 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb index 0f2a68be4b..b4fb5e015c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb index d44b604d27..9025d6b24b 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb index 248cce692e..2ac7d84426 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb index 83ed95495c..a7a958a3ca 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb index 8f07608f03..26fbe953cd 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb index 8d013d1941..84e658abed 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb index 4a22f26fd3..62ec508192 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb index a94a92c657..f56094b5c0 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb index 07838d8020..df9a262ab2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb index fd30e9820c..9082a71a46 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb index 39be41a74e..a2164fa02d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb index 1fe6136b55..8fa4a0a750 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb index 629ec16acb..1774b8976c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb index 15551872f9..d990801ac2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb index 4047b50760..97801124aa 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb index 2528629319..81d586f625 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb @@ -11,10 +11,10 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/v/vsc-base/', - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index b11b8ff6c1..cb8c19e606 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -11,10 +11,10 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/v/vsc-base/', - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb index 757c5d4553..4d3d248af6 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb @@ -13,8 +13,8 @@ scheduling; coroutines, in other words. This is useful when you want to control toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] -sources = ['%s-%s.zip' % (name.lower(), version)] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] python = "Python" pythonversion = '2.7.6' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f06323716c..46c4f977e8 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb index 88fdc36fa5..e37ffbc4e2 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb index 4707146708..191856a900 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb index a801441c8b..9711dba080 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb index 1dfd105d74..d4224bd978 100644 --- a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'monty' version = '0.6.4' -homepage = 'http://pypi.python.org/pypi/monty/' +homepage = 'https://pypi.python.org/pypi/monty/' description = """Monty implements supplementary useful functions for Python that are not part of the standard library. Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton and cached_class, and many more.""" diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb index 7d2b055f0b..58d8cae9ee 100644 --- a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'monty' version = '0.6.4' -homepage = 'http://pypi.python.org/pypi/monty/' +homepage = 'https://pypi.python.org/pypi/monty/' description = """Monty implements supplementary useful functions for Python that are not part of the standard library. Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton and cached_class, and many more.""" diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb index bd74a7c6d1..580a294eee 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "PyYAML" version = "3.11" -homepage = "http://pypi.python.org/pypi/PyYAML/" +homepage = "https://pypi.python.org/pypi/PyYAML/" description = """PyYAML is a YAML parser and emitter for the Python programming language.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 5625804833..8bf00ee94a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index eea5ccfa5e..2ade7ad4f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index a6794c06c9..a73fef035d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index dc891b7530..2af2f0c181 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index 51cfbe4606..0218dcafbd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 311b197edf..342b19c101 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index 80c8900b94..b883b3a7a7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index f847189fab..53fb8ff292 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index b2a76a28d3..c2cc52183e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 077f9d9e7e..994f20889f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 930a85f683..459199e8c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index f86e562788..3e4b4f03f3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 401dc6dd76..2e8be6d925 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index e19d9c8443..c6d6010f0e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 91d0cee83b..2da448273b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index 31732a9f47..b7849aec58 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 3dd0016674..c17df2cb09 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -52,7 +52,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -68,7 +68,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index 47b8de7acf..9f5cd7d95f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index a9868e2f66..a24d0b3e6e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index b3e31e4ea3..cee2b8e189 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -67,7 +67,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index ec5e6c7a3a..751a483994 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -65,7 +65,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 4625232be8..8b46b16cd3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -65,7 +65,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index 1496901c99..ed13d94285 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -53,7 +53,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -69,7 +69,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index ba61389fd5..8e7a62f6da 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.4.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index 575fabb0e6..aaba09ba09 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.4.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -67,7 +67,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 8b621ebdee..d9f7ad0b77 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.4.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -67,7 +67,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 8ef1b28d6b..6e042b928d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 2dd2282def..09dc45c1e6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,16 +48,16 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('six', '1.7.3', { - 'source_urls': ['http://pypi.python.org/packages/source/s/six/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 478804a887..383b7d978b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -34,13 +34,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -52,13 +52,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -74,7 +74,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index 54d5edce60..18aa12a4b8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 65ec137785..787f5ecab1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index ad901ece9f..16a9eea25f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -30,13 +30,13 @@ dependencies = [ # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,13 +48,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index 4ef1c682d1..fdb44db0d0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -31,13 +31,13 @@ buildopts = 'LINKCC="$CC -dynamic"' # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index adcd0caa18..bb0be0ac85 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -31,13 +31,13 @@ buildopts = 'LINKCC="$CC -dynamic"' # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index deac7ecaca..3950c920d4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -31,13 +31,13 @@ buildopts = 'LINKCC="$CC -dynamic"' # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index d228f95a16..3273aa0399 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -45,13 +45,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index e667c4f618..9a1f9af5fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -45,13 +45,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 06dcabeb70..95f4d38205 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,13 +48,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -73,7 +73,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index ff366c2d52..033d183105 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -27,14 +27,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index 1a46862919..c928dc3ca3 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -27,14 +27,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index bfaa166f08..f523509a1d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -29,14 +29,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 92a41bf7e7..a47ee809f5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -27,14 +27,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index c462546fe3..f23e383d17 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb index 51dd82cdf9..28d140c742 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index f1f4f3af6b..a66a2c142a 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index b64218f00f..07f5694321 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -73,7 +73,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 5769376b00..ba75d726f9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -73,7 +73,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 3265a5bd15..c5e5b4ddcb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev')] exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') exts_list = [ ('setuptools', '15.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,13 +48,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], @@ -73,7 +73,7 @@ exts_list = [ }), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb index 350eeb2738..7d470be431 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.11.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb index 683efb783b..644c39f1d8 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.11.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb index 9d8a5aeb67..236486c7f6 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.11.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb index b38ad74c90..934bb24741 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.12.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb index f0ae8b6a9f..36528b21fe 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.13.1" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb index d8f4627e56..a94b0b1e5d 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.16.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index dd8127de7f..05e281d1d7 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,15 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb index c1a1ef52b4..67f7bc47b5 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -3,14 +3,12 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb index 9d393ee393..0f1fade586 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb @@ -3,15 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb index 295d530de8..5170a4d2bd 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb @@ -3,16 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb index 66535a0069..f140852405 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb @@ -3,15 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'iomkl', 'version': '4.6.13'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb index 8e35e9a845..5534c8acd7 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'pymatgen' version = '3.0.13' -homepage = 'http://pypi.python.org/pypi/pymatgen' +homepage = 'https://pypi.python.org/pypi/pymatgen' description = """Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes.""" diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb index 73ac37040a..31bebaefdd 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'pymatgen' version = '3.0.13' -homepage = 'http://pypi.python.org/pypi/pymatgen' +homepage = 'https://pypi.python.org/pypi/pymatgen' description = """Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes.""" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 5e2b080c59..637462ec29 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,12 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb index ca5228d480..517404e770 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb @@ -3,12 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb index d34f8f5f64..62aa6e2bbc 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb @@ -3,12 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb index 612cf670c0..82de605fe3 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb @@ -3,13 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb index 87db02a9fa..f08e79381b 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb @@ -3,12 +3,12 @@ easyblock = "VersionIndependentPythonPackage" name = "setuptools" version = "1.4.2" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://pypi.python.org/packages/source/s/%(name)s/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb index 04c3e47988..241a1d5fbf 100644 --- a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "stemming" version = "1.0" -homepage = "http://pypi.python.org/pypi/stemming/" +homepage = "https://pypi.python.org/pypi/stemming/" description = """Python implementations of the Porter, Porter2, Paice-Husk, and Lovins stemming algorithms for English.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -- GitLab From 86662e26ed3675e7b71af0f4ccb419405765feea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 19:06:22 +0200 Subject: [PATCH 447/992] use PIPY_SOURCE as source URL where applicable --- .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb | 4 ++-- .../c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb | 4 ++-- .../c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 4 ++-- .../h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb | 2 +- 14 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb index 77441b5881..c519419dcf 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -17,8 +17,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cutadapt.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb index e788568341..f278de669b 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb @@ -17,8 +17,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cutadapt.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.5' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb index cf67752ee4..a308b21130 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb index 3a32415096..a4f5169761 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb @@ -17,8 +17,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.5' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb index f9435f3efa..3303167a21 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb index 8a431e4a45..dbc8a13634 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb @@ -12,8 +12,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://pypi.python.org/packages/source/c/cutadapt/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb index b165a51c0c..83a8d8a50d 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb index fbe7a035d3..f879b0939f 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb index a5093a2f21..60048badc4 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb index 737e7e93bb..a69f7bc2f8 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.9' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb index 467ed7ee6d..e1391aa56b 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb index d593001ecd..285c21b3f7 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb index 478d636658..411df518d3 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb index 172dead842..8894ccbab9 100644 --- a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb @@ -8,7 +8,7 @@ description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['https://pypi.python.org/packages/source/n/netaddr/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From a6ab388623360535963811b931c41ba15464ea94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2015 09:20:02 +0200 Subject: [PATCH 448/992] add easyconfig for binary version of FDS --- .../easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb new file mode 100644 index 0000000000..f0c7225183 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'FDS' +version = '6.0.1' +versionsuffix = '-no-OFED' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """ + Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and + heat transport from fires. +""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download .sh from https://bintray.com/nist-fire-research/releases/FDS-SMV/6.0.1/view/files to create tarball +sources = ['FDS_6.0.1-SMV_6.1.5_linux64.tar.gz'] + +dependencies = [('OpenMPI', '1.6.5-GCC-4.8.2-no-OFED')] + +skipsteps= ['configure', 'build'] + +sanity_check_paths = { + 'files': ['bin/fds', 'bin/fds_mpi'], + 'dirs': [], +} + +moduleclass = 'phys' -- GitLab From c52300e394b9cf0b7c924631155921ab7ee278f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2015 09:41:41 +0200 Subject: [PATCH 449/992] rename FDS patch file + style cleanup --- .../easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 9 ++++----- .../easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb | 12 ++++++------ ...{FDS_makefile.patch => FDS-r18915_makefile.patch} | 0 3 files changed, 10 insertions(+), 11 deletions(-) rename easybuild/easyconfigs/f/FDS/{FDS_makefile.patch => FDS-r18915_makefile.patch} (100%) diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb index d49cfa69e6..5747ab3226 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -2,20 +2,19 @@ name = 'FDS' version = 'r18915' homepage = 'https://code.google.com/p/fds-smv/' -description = """ - Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and - heat transport from fires. -""" +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + # just run make in the install dir skipsteps = ['configure', 'install'] buildininstalldir = True -patches = ['FDS_makefile.patch'] modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb index ef3f6f0041..9710fba50f 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb @@ -2,19 +2,19 @@ name = 'FDS' version = 'r18915' homepage = 'https://code.google.com/p/fds-smv/' -description = """ - Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and - heat transport from fires. -""" -toolchain = {'name': 'ictce', 'version': '5.5.0'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + # just run make in the install dir skipsteps = ['configure', 'install'] buildininstalldir = True -patches = ['FDS_makefile.patch'] modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FDS/FDS_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch similarity index 100% rename from easybuild/easyconfigs/f/FDS/FDS_makefile.patch rename to easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch -- GitLab From 41b4371583caa928a9519cdaa614e4970ad46880 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2015 09:44:50 +0200 Subject: [PATCH 450/992] add missing 'easyblock' line --- easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb index 5747ab3226..e84a122aeb 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'FDS' version = 'r18915' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb index 9710fba50f..78ff82e688 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'FDS' version = 'r18915' -- GitLab From 0a5a707410bc0c3fab77da9a0ee24053a53a7802 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 19 May 2015 14:04:48 +0200 Subject: [PATCH 451/992] os dependency added --- easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb index b64ac043f3..3efae98cdb 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb @@ -20,6 +20,8 @@ builddependencies = [ ('gperf', '3.0.4'), ] +osdependencies = [('kernel-headers','linux-libc-dev')] + configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' preinstallopts = "make check && " -- GitLab From b2a2986eb682f37726eee7a591584422cdabc52b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2015 15:52:28 +0200 Subject: [PATCH 452/992] {vis}[intel/2015a] frealign 9.09 --- .../frealign-9.09-intel-2015a-avx-mp.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb diff --git a/easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb b/easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb new file mode 100644 index 0000000000..a6b21fbfff --- /dev/null +++ b/easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'frealign' +version = '9.09' +versionsuffix = '-avx-mp' + +homepage = 'http://grigoriefflab.janelia.org/frealign' +description = """Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of + single particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] +sources = ['frealign_v%(version)s_150422.tar.gz'] + +start_dir = 'src' + +parallel = 1 + +# clean all included binaries first +prebuildopts = "rm ../bin/* && " +buildopts = "-f Makefile_linux_avx_intel_mp_static" + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/resample_mp.exe', 'bin/merge_3d_mp.exe', 'bin/frealign_v%(version_major)s_mp.exe'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 5854c953b9f93d8d38e508d64971d6b0a4d22505 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 May 2015 08:29:18 +0200 Subject: [PATCH 453/992] with intel-2015a as well --- .../e/eudev/eudev-3.0-intel-2015a.eb | 33 +++++++++++++++++++ .../g/gperf/gperf-3.0.4-intel-2015a.eb | 22 +++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb new file mode 100644 index 0000000000..9ada9135c9 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.0' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-%(version)s_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers','linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +preinstallopts = "make check && " + +sanity_check_paths = { + 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs' : [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.eb new file mode 100644 index 0000000000..03d48cbdf1 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 53337ee42f174c2358b16c68a3caf3022e462e1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 09:12:01 +0200 Subject: [PATCH 454/992] rework foss/2015.01 by introducing GNU subtoolchain --- .../Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb | 26 ++++++++++ .../Automake/Automake-1.15-GNU-4.9.2-2.25.eb | 33 ++++++++++++ ... binutils-2.25-GCC-4.9.2-binutils-2.25.eb} | 4 +- .../f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb | 34 ------------- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 14 ++--- .../g/GCC/GCC-4.9.2-binutils-2.25.eb | 45 ++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb | 2 - easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb | 20 ++++++++ easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb | 23 --------- .../easyconfigs/g/gompi/gompi-2015.01.eb | 12 ++--- easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb | 38 -------------- .../easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb | 18 ------- .../h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb | 23 +++++++++ .../l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb | 15 ++++++ .../m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb | 23 +++++++++ .../numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb | 31 +++++++++++ ...BLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 51 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb | 34 +++++++++++++ ...ompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 25 --------- .../zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 21 ++++++++ 20 files changed, 337 insertions(+), 155 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb rename easybuild/easyconfigs/b/binutils/{binutils-2.25-GCC-4.9.2.eb => binutils-2.25-GCC-4.9.2-binutils-2.25.eb} (85%) delete mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb delete mode 100644 easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb delete mode 100644 easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb delete mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb delete mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..b57c1dcc83 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..f0e456c431 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb similarity index 85% rename from easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb rename to easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index f91dda00cd..9fe47929d3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -9,11 +9,11 @@ description = "binutils: GNU binary utilities" sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-%(version)s'} dependencies = [('zlib', '1.2.8')] -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', version, '', True)] configopts = '--with-sysroot' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb deleted file mode 100644 index 080b817838..0000000000 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'FFTW' -version = '3.3.4' - -homepage = 'http://www.fftw.org' -description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) - in one or more dimensions, of arbitrary input size, and of both real and complex data.""" - -toolchain = {'name': 'gompi', 'version': '1.9.0'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [homepage] - -common_configopts = "--enable-threads --enable-openmp --with-pic" - -configopts = [ - common_configopts + " --enable-single --enable-sse2 --enable-mpi", - common_configopts + " --enable-long-double --enable-mpi", - common_configopts + " --enable-quad-precision", - common_configopts + " --enable-sse2 --enable-mpi", # default as last -] - -sanity_check_paths = { - 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb index 9c0f07775d..47df95ad70 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -9,9 +9,9 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, includi toolchain = {'name': 'dummy', 'version': 'dummy'} -comp_name = 'GCC' -comp_version = '4.9.2' -comp = (comp_name, comp_version) +gccver = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) blaslib = 'OpenBLAS' blasver = '0.2.13' @@ -28,10 +28,10 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # because of toolchain preperation functions # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ - comp, - ('binutils', '2.25', '', comp), - ('OpenMPI', '1.8.4', '', comp), - (blaslib, blasver, blassuff, comp), + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.4', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), ] diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000..4985b9228e --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,45 @@ +name = "GCC" +version = '4.9.2' + +binutilsver = '2.25' +versionsuffix = '-binutils-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +builddependencies = [('binutils', binutilsver)] + +patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index dd71a77ce5..ebf339e6b0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -22,8 +22,6 @@ sources = [ 'mpc-1.0.2.tar.gz', ] -builddependencies = [('binutils', '2.25')] - patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] checksums = [ diff --git a/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..c1b036b3c1 --- /dev/null +++ b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'GNU' +gccver = '4.9.2' +binutilsver = '2.25' +version = '%s-%s' % (gccver, binutilsver) + +homepage = 'http://gnu.org' +description = "Compiler-only toolchain with GCC and binutils." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # GCC built on top of (dummy-built) binutils + ('GCC', gccver, '-binutils-%s' % binutilsver), + # binutils built on top of GCC, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCC', '%s-binutils-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb deleted file mode 100644 index f8cc89cff5..0000000000 --- a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = "Toolchain" - -name = 'gompi' -version = '1.9.0' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, - including OpenMPI for MPI support.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -compname = 'GCC' -compver = '4.9.2' -comp = (compname, compver) - -# compiler toolchain dependencies -dependencies = [ - comp, - ('binutils', '2.25', '', comp), - ('OpenMPI', '1.8.4', '', comp), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb index 1dd2af3813..61953c785a 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb @@ -9,15 +9,15 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, toolchain = {'name': 'dummy', 'version': 'dummy'} -compname = 'GCC' -compver = '4.9.2' -comp = (compname, compver) +gccver = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) # compiler toolchain dependencies dependencies = [ - comp, - ('binutils', '2.25', '', comp), - ('OpenMPI', '1.8.4', '', comp), + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.4', '', ('GNU', '%s-%s' % (gccver, binutilsver))), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb deleted file mode 100644 index feeb6330ff..0000000000 --- a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = "Toolchain" - -name = 'goolf' -version = '1.9.0' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, including - OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -comp_name = 'GCC' -comp_version = '4.9.2' -comp = (comp_name, comp_version) - -blaslib = 'OpenBLAS' -blasver = '0.2.13' -blas = '%s-%s' % (blaslib, blasver) -blassuff = '-LAPACK-3.5.0' - -# toolchain used to build goolf dependencies -comp_mpi_tc_name = 'gompi' -comp_mpi_tc_ver = "%s" % version -comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) - -# compiler toolchain depencies -# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain -# because of toolchain preperation functions -dependencies = [ - comp, - ('binutils', '2.25', '', comp), - ('OpenMPI', '1.8.4', '', comp), - (blaslib, blasver, blassuff, comp), - ('FFTW', '3.3.4', '', comp_mpi_tc), - ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb deleted file mode 100644 index e9fc6dc2e2..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'goolf', 'version': '1.9.0'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..dfcbd3f2c0 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.10.0' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +dependencies = [('numactl', '2.0.10')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..9897d9bd11 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.2' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..e2764250bf --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..3ada055448 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.10' + +checksums = ['682c38305b2596967881f3d77bc3fc9c'] + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('Automake', '1.15'), + ('libtool', '2.4.2'), +] + +preconfigopts = './autogen.sh && ' + + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..1ff75dff8d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.13' + +lapackver = '3.5.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..14daf056ee --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.4' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.10.0')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", + "mpi", "ompitrace", "open-pal", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb deleted file mode 100644 index e0aff023b0..0000000000 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'ScaLAPACK' -version = '2.0.2' - -homepage = 'http://www.netlib.org/scalapack/' -description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines - redesigned for distributed memory MIMD parallel computers.""" - -toolchain = {'name': 'gompi', 'version': '1.9.0'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TGZ] - -blaslib = 'OpenBLAS' -blasver = '0.2.13' -blassuff = '-LAPACK-3.5.0' - -versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) - -dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.2'))] - -## parallel build tends to fail, so disabling it -parallel = 1 - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000..64ff4fbec6 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 63c37d0acd168b26d30710221f45fc7da541f7cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 09:21:03 +0200 Subject: [PATCH 455/992] fix ScaLAPACK dep spec --- ...caLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb index 962d8049d0..cd879dacd3 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -17,7 +17,7 @@ blassuff = '-LAPACK-3.5.0' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.2'))] +dependencies = [(blaslib, blasver, blassuff, ('GNU', '4.9.2-2.25'))] ## parallel build tends to fail, so disabling it parallel = 1 -- GitLab From 1009235604f4daa0eb83b0dd659c66d0f8ffe7d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:06:28 +0200 Subject: [PATCH 456/992] add Tk without X11 support --- .../t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb new file mode 100644 index 0000000000..50b6df47b2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 206c5f6ff26612114751151767a7e9ebc9c2f220 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:15:39 +0200 Subject: [PATCH 457/992] remove libX11 dep from no-X11 Tk easyconfig --- easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb index 50b6df47b2..39ccca9596 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -15,7 +15,6 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), - ('libX11', '1.6.3', '-Python-2.7.9'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' -- GitLab From 9f1645c4cc7b5494284c4c8b8b0531a5aa31f168 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:33:06 +0200 Subject: [PATCH 458/992] use --with-sysroot=/ in binutils easyconfigs --- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 3 ++- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 9fe47929d3..b93783f696 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,8 @@ dependencies = [('zlib', '1.2.8')] builddependencies = [('binutils', version, '', True)] -configopts = '--with-sysroot' +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 9a9d28a75d..dee468601d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -17,7 +17,8 @@ builddependencies = [('zlib', '1.2.8')] preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -configopts = '--with-sysroot' +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] -- GitLab From becefcb5a6635e5df687e18c59313044ddddd775 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:44:22 +0200 Subject: [PATCH 459/992] use no-X11 Tk as dep in R-extra easyconfig --- .../R-extra-20150323-intel-2015a-R-3.1.3.eb | 2 +- .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 ------------------- .../easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb | 24 ------------------ 3 files changed, 1 insertion(+), 50 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb index 7ec2e95168..6cd16e2bf9 100644 --- a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb @@ -17,7 +17,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), ('Tcl', '8.6.4'), - ('Tk', '8.6.4'), + ('Tk', '8.6.4', '-no-X11'), ('cURL', '7.41.0'), ('libxml2', '2.9.2'), ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb deleted file mode 100644 index b2673863fd..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb deleted file mode 100644 index de684154a7..0000000000 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tk' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building - a graphical user interface (GUI) in many different programming languages.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('Tcl', version), - ('libX11', '1.6.3', '-Python-2.7.9'), -] - -configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' - -start_dir = 'unix' - -moduleclass = 'vis' -- GitLab From f0b88162888cec97df7788b437445f0f98efaa82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 12:00:37 +0200 Subject: [PATCH 460/992] readd Tcl 8.6.4 that is required as a dep --- .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..b2673863fd --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From ca15317769e216045f32651ab9e9b199fcbf3671 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 14:42:01 +0200 Subject: [PATCH 461/992] fix typo --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 838f4a2957..6efa3b178f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -244,7 +244,7 @@ def template_easyconfig_test(self, spec): # check easyconfig file name expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) - msg = "Filename '%s' of parsed easconfig matches expected filename '%s'" % (spec, expected_fn) + msg = "Filename '%s' of parsed easyconfig matches expected filename '%s'" % (spec, expected_fn) self.assertEqual(os.path.basename(spec), expected_fn, msg) name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) -- GitLab From 6c6c63d9e27c12d2ae6b99f88af11fbd8cf28637 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 20 May 2015 13:41:12 +0200 Subject: [PATCH 462/992] WIP for R-bundles and devtools. Renaming the file and giving it a fix for the versionsuffix. Updated to reflect boegel's comment. --- ...s-20150520-intel-2015a-R-3.1.3-devtools.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb diff --git a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb new file mode 100644 index 0000000000..cf38b2b642 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'R-bundles' +version = '20150520' +bundlename = 'devtools' +rver = '3.1.3' +versionsuffix = '-R-%s-%s' % (rver, bundlename) + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('cURL', '7.41.0'), + ('libxml2', '2.9.2'), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('XML', '3.98-1.1', ext_options), + ('memoise', '0.2.1', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.3.1', ext_options), + ('roxygen2', '4.1.1', ext_options), + ('git2r', '0.10.1', ext_options), + ('RCurl', '1.95-4.6', ext_options), + ('httr', '0.6.1', ext_options), + ('rversions', '1.0.0', ext_options), + ('devtools', '1.8.0', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' + -- GitLab From 0ad26a61082a6538d145fa4a1bef534cc383bcbe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 15:48:17 +0200 Subject: [PATCH 463/992] update to OpenMPI 1.8.5 and OpenBLAS 0.2.14 (foss/2015.05) --- .../Autotools-20150215-GNU-4.9.2-2.25.eb | 17 +++++++ ...2015.01.eb => FFTW-3.3.4-gompi-2015.05.eb} | 2 +- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 39 -------------- easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb | 2 +- .../easyconfigs/g/gompi/gompi-2015.01.eb | 23 --------- .../h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb | 23 --------- .../l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb | 15 ------ .../numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb | 6 +-- ...BLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 51 ------------------- .../o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb | 34 ------------- ...i-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb} | 4 +- 11 files changed, 22 insertions(+), 194 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.4-gompi-2015.01.eb => FFTW-3.3.4-gompi-2015.05.eb} (96%) delete mode 100644 easybuild/easyconfigs/f/foss/foss-2015.01.eb delete mode 100644 easybuild/easyconfigs/g/gompi/gompi-2015.01.eb delete mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb delete mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb delete mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb => ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb} (89%) diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..25b293c3c4 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.05.eb similarity index 96% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.05.eb index bcb190c092..0d9c4ae7b5 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.05.eb @@ -7,7 +7,7 @@ homepage = 'http://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'gompi', 'version': '2015.01'} +toolchain = {'name': 'gompi', 'version': '2015.05'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb deleted file mode 100644 index 47df95ad70..0000000000 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = "Toolchain" - -name = 'foss' -version = '2015.01' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, including - OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -gccver = '4.9.2' -binutilsver = '2.25' -tcver = '%s-binutils-%s' % (gccver, binutilsver) - -blaslib = 'OpenBLAS' -blasver = '0.2.13' -blas = '%s-%s' % (blaslib, blasver) -blassuff = '-LAPACK-3.5.0' - -# toolchain used to build foss dependencies -comp_mpi_tc_name = 'gompi' -comp_mpi_tc_ver = "%s" % version -comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) - -# compiler toolchain depencies -# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain -# because of toolchain preperation functions -# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds -dependencies = [ - ('GCC', gccver, '-binutils-%s' % binutilsver), - ('binutils', binutilsver, '', ('GCC', tcver)), - ('OpenMPI', '1.8.4', '', ('GNU', '%s-%s' % (gccver, binutilsver))), - (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), - ('FFTW', '3.3.4', '', comp_mpi_tc), - ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb index c1b036b3c1..61b0e08a72 100644 --- a/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb @@ -5,7 +5,7 @@ gccver = '4.9.2' binutilsver = '2.25' version = '%s-%s' % (gccver, binutilsver) -homepage = 'http://gnu.org' +homepage = 'http://www.gnu.org/software/' description = "Compiler-only toolchain with GCC and binutils." toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb deleted file mode 100644 index 61953c785a..0000000000 --- a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = "Toolchain" - -name = 'gompi' -version = '2015.01' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, - including OpenMPI for MPI support.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -gccver = '4.9.2' -binutilsver = '2.25' -tcver = '%s-binutils-%s' % (gccver, binutilsver) - -# compiler toolchain dependencies -dependencies = [ - ('GCC', gccver, '-binutils-%s' % binutilsver), - ('binutils', binutilsver, '', ('GCC', tcver)), - ('OpenMPI', '1.8.4', '', ('GNU', '%s-%s' % (gccver, binutilsver))), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb deleted file mode 100644 index dfcbd3f2c0..0000000000 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.10.0' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction - (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including - NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various - system attributes such as cache and memory information as well as the locality of I/O devices such as - network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering - information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} - -dependencies = [('numactl', '2.0.10')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb deleted file mode 100644 index 9897d9bd11..0000000000 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb +++ /dev/null @@ -1,15 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libtool' -version = '2.4.2' - -homepage = 'http://www.gnu.org/software/libtool' -description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries - behind a consistent, portable interface.""" - -toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb index 3ada055448..52f1df7369 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb @@ -15,14 +15,10 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] -builddependencies = [ - ('Automake', '1.15'), - ('libtool', '2.4.2'), -] +builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' - sanity_check_paths = { 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], 'dirs': ['share/man', 'include'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb deleted file mode 100644 index 1ff75dff8d..0000000000 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OpenBLAS' -version = '0.2.13' - -lapackver = '3.5.0' -versionsuffix = '-LAPACK-%s' % lapackver - -homepage = 'http://xianyi.github.com/OpenBLAS/' -description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" - -toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} - -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] -source_urls = [ - # order matters, trying to download the LAPACK tarball from GitHub causes trouble - "http://www.netlib.org/lapack/", - "http://www.netlib.org/lapack/timing/", - "https://github.com/xianyi/OpenBLAS/archive/", -] - -patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), -] - -skipsteps = ['configure'] - -buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' -installopts = "USE_THREAD=1 PREFIX=%(installdir)s" - -# extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' - -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb deleted file mode 100644 index 14daf056ee..0000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OpenMPI' -version = '1.8.4' - -homepage = 'http://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-2 implementation.""" - -toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - -dependencies = [('hwloc', '1.10.0')] - -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' -configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support -configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading - -# needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + - ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], -} - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb similarity index 89% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb index cd879dacd3..e8390ed236 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb @@ -5,14 +5,14 @@ homepage = 'http://www.netlib.org/scalapack/' description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.""" -toolchain = {'name': 'gompi', 'version': '2015.01'} +toolchain = {'name': 'gompi', 'version': '2015.05'} toolchainopts = {'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' -blasver = '0.2.13' +blasver = '0.2.14' blassuff = '-LAPACK-3.5.0' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -- GitLab From 36303e1d582c3fd5e68fae3d6d28c3b3fdc60711 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 15:58:31 +0200 Subject: [PATCH 464/992] add missing easyconfigs --- .../easyconfigs/g/gompi/gompi-2015.05.eb | 23 +++++++++ .../l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb | 15 ++++++ ...BLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 51 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 34 +++++++++++++ 4 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2015.05.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb new file mode 100644 index 0000000000..a9acbdd507 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2015.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..2985ab6f8a --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..23704a985e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.14' + +lapackver = '3.5.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..17455567fb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.5' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.10.1')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", + "mpi", "ompitrace", "open-pal", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From 324627c42123041813559bf922af272a562e7d65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 16:06:20 +0200 Subject: [PATCH 465/992] add missing hwloc, also update HPL easyconfig for foss/2015.05 --- ...oss-2015.01.eb => HPL-2.1-foss-2015.05.eb} | 2 +- .../h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb | 23 +++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.1-foss-2015.01.eb => HPL-2.1-foss-2015.05.eb} (92%) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb similarity index 92% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb index 6e2eb261d6..6e7b16eb21 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'foss', 'version': '2015.01'} +toolchain = {'name': 'foss', 'version': '2015.05'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..33b2aeafd6 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.10.1' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +dependencies = [('numactl', '2.0.10')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' -- GitLab From 217d5da8dc55d077a2acb7ba42db1a0ffc2896b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 16:15:07 +0200 Subject: [PATCH 466/992] add foss/2015.05 easyconfig --- easybuild/easyconfigs/f/foss/foss-2015.05.eb | 39 ++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2015.05.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2015.05.eb b/easybuild/easyconfigs/f/foss/foss-2015.05.eb new file mode 100644 index 0000000000..e468cc0b43 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2015.05.eb @@ -0,0 +1,39 @@ +easyblock = "Toolchain" + +name = 'foss' +version = '2015.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +blaslib = 'OpenBLAS' +blasver = '0.2.14' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' -- GitLab From afa60d29df4fe8302f4ec69816fa2cfbe8b0415f Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 20 May 2015 16:45:41 +0200 Subject: [PATCH 467/992] Roll back the cURL version since 7.41.0 is parked in a WIP PR. --- .../R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb index cf38b2b642..8cb259acf8 100644 --- a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -17,7 +17,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('cURL', '7.41.0'), + ('cURL', '7.40.0'), ('libxml2', '2.9.2'), ] -- GitLab From 6947b4af64d910b5b3586d4a29c4a12a458384b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 16:54:47 +0200 Subject: [PATCH 468/992] don't fiddle with existing GCC-4.9.2.eb easyconfig --- easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index ebf339e6b0..cb9f3aa4f2 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' -- GitLab From 19101529562e7a25335428c780ab6320c6bcabbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 16:59:04 +0200 Subject: [PATCH 469/992] readd binutils easyconfig that was there already --- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb new file mode 100644 index 0000000000..e44a4bc4f7 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +dependencies = [ + ('zlib', '1.2.8'), +] + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 2acb0acb676ef4263c9e9b41c07626935db96886 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 17:08:03 +0200 Subject: [PATCH 470/992] add --with-sysroot=/ to all binutils easyconfigs --- .../b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb | 7 +++++-- .../b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb | 7 +++++-- .../easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb | 5 ++++- .../easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb | 3 +++ .../easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb | 3 +++ .../easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 3 +++ 6 files changed, 23 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index 6d0b4d9315..09be4e2513 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -18,11 +18,14 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} + sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'pic': True} +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 129afa50d1..037eea64d6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -18,11 +18,14 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True} + sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -toolchainopts = {'pic': True} +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index 98ff0c9aef..6eefeecf7f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -18,10 +18,13 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -toolchain = {'name': 'goolf', 'version': '1.4.10'} +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb index 7e0429c8a1..f289f62f1b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb @@ -15,6 +15,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 35ffa05491..90ee55811f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -15,6 +15,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + # disable warning/error #175 ("subscript out of range") buildopts = 'CFLAGS="$CFLAGS -wd175"' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index e44a4bc4f7..080795bcde 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -15,6 +15,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { -- GitLab From 948fa64a0701c1236890593168e3cf07d3e725a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 17:27:44 +0200 Subject: [PATCH 471/992] include Tcl and Tk as dependencies in R easyconfig --- .../easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 ++ .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 24 ++++++++++++++++++ 3 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 19bdf89c03..fefd97519c 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] name_tmpl = '%(name)s_%(version)s.tar.gz' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..b2673863fd --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb new file mode 100644 index 0000000000..39ccca9596 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 46e6b83f725bba2477cc26f82853bbe7b2d6376a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 18:22:29 +0200 Subject: [PATCH 472/992] Revert "don't bother committing foss version" This reverts commit b97ff1c4e5b44c4ea3f935b1d1ed1fbbcb67e668. --- .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 33 +++++++++++++++++++ .../r/Ruby/Ruby-2.1.5-intel-2014b.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb new file mode 100644 index 0000000000..c585ab1d31 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb @@ -0,0 +1,33 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.1.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +sanity_check_paths = { + 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'lib/libruby-static.a', 'lib/libruby.so'], + 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] +} + +configopts = "--disable-install-doc --enable-shared" + +moduleclass = 'lang' + diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb new file mode 100644 index 0000000000..32eca44aae --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb @@ -0,0 +1,33 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- +easyblock = 'ConfigureMake' + +name = 'Ruby' +version = '2.1.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +sanity_check_paths = { + 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'lib/libruby-static.a', 'lib/libruby.so'], + 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] +} + +configopts = "--disable-install-doc --enable-shared" + +moduleclass = 'lang' -- GitLab From c0e1547ae6e599aed6800950d34a54674ad0040c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 18:22:51 +0200 Subject: [PATCH 473/992] don't bother committing foss version (fixed) --- .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb deleted file mode 100644 index c585ab1d31..0000000000 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb +++ /dev/null @@ -1,33 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for Ruby 2.1: -# ---------------------------------------------------------------------------- -# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Aaron Zauner -# ---------------------------------------------------------------------------- - -name = 'Ruby' -version = '2.1.5' - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] - -sanity_check_paths = { - 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', - 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] -} - -configopts = "--disable-install-doc --enable-shared" - -moduleclass = 'lang' - -- GitLab From b6f710ac19644014cbec67d6e8c046af4b59ae0a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 May 2015 18:49:43 +0200 Subject: [PATCH 474/992] add missing build dep for binutils in zlib --- .../easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb index 64ff4fbec6..3f419579d9 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +builddependencies = [('binutils', '2.25', '', True)] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From 76f35e21156e30e817fa9dc9a55e95ce559a8239 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 May 2015 18:50:35 +0200 Subject: [PATCH 475/992] libtool was missing M4 dep --- easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb index 2985ab6f8a..f29d89e1c6 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb @@ -12,4 +12,6 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +dependencies = [('M4', '1.4.17')] + moduleclass = 'lib' -- GitLab From 627201ca872c434956e141ea54f1ae6b115ce694 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 May 2015 19:26:58 +0200 Subject: [PATCH 476/992] statically link zlib in binutils --- .../binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index b93783f696..f316e5d537 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -6,18 +6,23 @@ version = '2.25' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] - toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-%(version)s'} -dependencies = [('zlib', '1.2.8')] +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] -builddependencies = [('binutils', version, '', True)] +builddependencies = [ + ('zlib', '1.2.8'), + ('binutils', version, '', True) +] # make sure that system libraries are also considered by ld configopts = '--with-sysroot=/' +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] -- GitLab From 38ce9f64b23d7bdf5de4d590e4670b7c42a5dbbc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 May 2015 20:54:18 +0200 Subject: [PATCH 477/992] all binutils-2.25 link statically with zlib --- .../binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 6 +++--- .../easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 11 +++++++---- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 4 ++-- 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index f316e5d537..cb9289d4be 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -16,13 +16,13 @@ builddependencies = [ ('binutils', version, '', True) ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 080795bcde..8aefcfeeee 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -6,20 +6,23 @@ version = '2.25' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'GCC', 'version': '4.9.2'} +builddependencies = [('zlib', '1.2.8')] -dependencies = [ - ('zlib', '1.2.8'), -] +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index dee468601d..3c7395c4a9 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -6,11 +6,11 @@ version = '2.25' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" +toolchain = {'name': 'dummy', 'version': ''} + sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'dummy', 'version': ''} - builddependencies = [('zlib', '1.2.8')] # statically link with zlib, to avoid runtime dependency on zlib -- GitLab From f6913e1ca0c1873885fc8c49f7b1435f485d090c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 20:57:29 +0200 Subject: [PATCH 478/992] flesh out FPM into a dedicated easyconfig, sanity_check_paths were moved to Ruby easyblock --- .../easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb | 17 +++++++++++++++++ easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 14 +------------- 2 files changed, 18 insertions(+), 13 deletions(-) create mode 100644 easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb new file mode 100644 index 0000000000..a275aabe94 --- /dev/null +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb @@ -0,0 +1,17 @@ +easyblock = 'RubyGem' + +name = 'FPM' +version = '1.3.3' + +homepage = 'https://github.com/jordansissel/fpm' +description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease + and sanity.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://rubygems.org/downloads/'] +sources = ['%(namelower)s-%(version)s.gem'] + +dependencies = [('Ruby', '2.1.5')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb index d422f5a2f3..a83d1888f2 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -20,19 +20,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] -# Due to the way versioning works now with ruby, the libraries and such are labelled major.minor.0 -sanity_check_paths = { - 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.%(version_major_minor)s.0', - 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/%(version_major_minor)s.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-%(version_major_minor)s.0'] -} - - ext_options = { - 'source_urls': [ - 'http://rubygems.org/downloads/', # gem archive - ], + 'source_urls': ['http://rubygems.org/downloads/'], 'source_tmpl': '%(name)s-%(version)s.gem', } @@ -44,7 +33,6 @@ exts_list = [ ('backports', '3.6.4', ext_options), ('arr-pm', '0.0.9', ext_options), ('clamp', '0.6.4', ext_options), - ('fpm', '1.3.3', ext_options), ] moduleclass = 'lang' -- GitLab From 4dad61c9513cce50dd112e6e87c4ca4584e26049 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 21:16:37 +0200 Subject: [PATCH 479/992] bump versions: Ruby 2.1.6 + latest extension versions --- ...1.3.3-Ruby-2.1.5.eb => FPM-1.3.3-Ruby-2.1.6.eb} | 5 ++++- .../r/Ruby/{Ruby-2.1.5.eb => Ruby-2.1.6.eb} | 14 +++++++------- 2 files changed, 11 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/f/FPM/{FPM-1.3.3-Ruby-2.1.5.eb => FPM-1.3.3-Ruby-2.1.6.eb} (81%) rename easybuild/easyconfigs/r/Ruby/{Ruby-2.1.5.eb => Ruby-2.1.6.eb} (78%) diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb similarity index 81% rename from easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb rename to easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb index a275aabe94..b6d3efe3ac 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb @@ -3,6 +3,9 @@ easyblock = 'RubyGem' name = 'FPM' version = '1.3.3' +rubyver = '2.1.6' +versionsuffix = '-Ruby-%s' % rubyver + homepage = 'https://github.com/jordansissel/fpm' description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.""" @@ -12,6 +15,6 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://rubygems.org/downloads/'] sources = ['%(namelower)s-%(version)s.gem'] -dependencies = [('Ruby', '2.1.5')] +dependencies = [('Ruby', rubyver)] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb similarity index 78% rename from easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb rename to easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb index a83d1888f2..b2e22e2b13 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb @@ -8,7 +8,7 @@ # ---------------------------------------------------------------------------- name = 'Ruby' -version = '2.1.5' +version = '2.1.6' homepage = 'https://www.ruby-lang.org' description = """Ruby is a dynamic, open source programming language with @@ -26,13 +26,13 @@ ext_options = { } exts_list = [ - ('ffi', '1.9.6', ext_options), - ('childprocess', '0.5.5', ext_options), - ('json', '1.8.2', ext_options), - ('cabin', '0.7.1', ext_options), + ('ffi', '1.9.8', ext_options), + ('childprocess', '0.5.6', ext_options), + ('json', '1.8.2', ext_options), + ('cabin', '0.7.1', ext_options), ('backports', '3.6.4', ext_options), - ('arr-pm', '0.0.9', ext_options), - ('clamp', '0.6.4', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '0.6.5', ext_options), ] moduleclass = 'lang' -- GitLab From b78e23ea4e58b6aeb28fd761199985966487b8c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 22:03:41 +0200 Subject: [PATCH 480/992] include Tcl and Tk as dependencies in R foss/2015a easyconfig --- .../easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 2 ++ .../easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb | 24 ++++++++++++++++++ 3 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index ad11c875f8..5d7d661a1f 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] name_tmpl = '%(name)s_%(version)s.tar.gz' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb new file mode 100644 index 0000000000..d1a6b6efb2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb new file mode 100644 index 0000000000..fee35bd216 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From f2d25bea1c5399f3d5b22e2f25f915ab2adac5ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:05:19 +0200 Subject: [PATCH 481/992] {vis}[intel/2015a] SPIDER 22.10 --- .../s/SPIDER/SPIDER-22.10-intel-2015a.eb | 41 +++++++++++ .../SPIDER-22.10_fix-syntax-ifort.patch | 71 +++++++++++++++++++ 2 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb new file mode 100644 index 0000000000..f9744a6899 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -WB -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' +#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DSP_MP -c" LF="$F90FLAGS"' +#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DUSE_MPI -c" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch new file mode 100644 index 0000000000..9857ea9f14 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -0,0 +1,71 @@ +--- spider/src/copyfromtif.f.orig 2014-11-20 17:31:58.000000000 +0100 ++++ spider/src/copyfromtif.f 2015-05-20 20:18:45.688100002 +0200 +@@ -88,7 +88,7 @@ + INTEGER(KIND=1), ALLOCATABLE :: I1VALS(:) + INTEGER(KIND=4), ALLOCATABLE :: I4VALS(:) + +- CHARACTER(LEN=1), ALLOCATABLE :: CVAL(:) ++ CHARACTER(LEN=:), ALLOCATABLE :: CVAL + + CHARACTER(LEN=24) :: CDATE + +@@ -290,7 +290,7 @@ + IF ( ICOUNT > ICVAL_LEN) THEN + IF (ALLOCATED(CVAL)) DEALLOCATE(CVAL) + ICVAL_LEN = ICOUNT +- ALLOCATE(CVAL(1)(ICVAL_LEN), STAT=IRTFLG) ++ ALLOCATE(CHARACTER(LEN=ICVAL_LEN) :: CVAL, STAT=IRTFLG) + + IF (IRTFLG .NE. 0) THEN + CALL ERRT(46,'COPYFROMTIF; CVAL...',ICVAL_LEN) +@@ -432,7 +432,7 @@ + GOTRESU = .TRUE. + + ELSEIF (ITAG == 306) THEN +- CDATE = CVAL(1)(1:22) ++ CDATE = CVAL(1:22) + c IF (DEBUG) WRITE(NOUT,'(2X,A,1X,200A)')'DATE & TIME:', + c & CVAL(1)(1:ICOUNT) + GOTDATE = .TRUE. +--- spider/src/copypos.f.orig 2015-05-20 21:21:12.693293000 +0200 ++++ spider/src/copypos.f 2015-05-20 21:21:37.499077116 +0200 +@@ -269,7 +269,7 @@ + ENDIF + + C GREATER OF (0 AND (THE SMALLER OF RVAL AND 255)) +- IVAL = MAX(0,MIN(RVAL, 255.)) ++ IVAL = MAX(0.,MIN(RVAL, 255.)) + + IF (FLIP) THEN + IVAL = 255 - IVAL +--- spider/src/hisd.f.orig 2015-05-20 21:30:04.788208000 +0200 ++++ spider/src/hisd.f 2015-05-20 21:30:29.848221000 +0200 +@@ -146,9 +146,7 @@ + & 'OUTPUT DOC FILE (OR * IF NONE)',ISOLD,APPEND,MESSAGE, + & NEWFILE,IRTFLG) + +- WANTDOC = (IRTFLG == 0) +- +- IF (WANTDOC) THEN ++ IF (IRTFLG == 0) THEN + C OUTPUT TO DOC FILE + + C 123456789 123456789 123456789 123456789 123456789 +--- spider/src/star2doc.f.orig 2015-05-20 21:41:24.588241000 +0200 ++++ spider/src/star2doc.f 2015-05-20 21:41:50.069338858 +0200 +@@ -82,6 +82,7 @@ + CHARACTER(LEN=1) :: CDUM + INTEGER :: LUNDOCT,ILOC,IT,NLIST,ILAST + INTEGER :: IHI,I,IKEY,IRTFLG,LENREC,IVAR,ITOK ++ INTEGER :: NSPI + + LOGICAL :: ISOPEN,EX,CALLERRT,ASKNAM + LOGICAL :: ADDEXT,GETNAME +--- /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 ++++ /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 +@@ -14,4 +14,4 @@ + .f.a: + $(COMP) $(FFLAGS) $< + $(AR) $(AFLAGS) $(LIB) $*.o +- @\rm $*.o ++# @\rm $*.o -- GitLab From b1b0d1ed44844db6e5e773b53ea20a18b485f6f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:06:21 +0200 Subject: [PATCH 482/992] fix path in SPIDER patch --- .../easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch index 9857ea9f14..3f36cf0b41 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -61,8 +61,8 @@ LOGICAL :: ISOPEN,EX,CALLERRT,ASKNAM LOGICAL :: ADDEXT,GETNAME ---- /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 -+++ /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 +--- spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 ++++ spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 @@ -14,4 +14,4 @@ .f.a: $(COMP) $(FFLAGS) $< -- GitLab From a54658145a7cfe4633c9958ede6b2d7e44defd23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:40:43 +0200 Subject: [PATCH 483/992] add -mt and -mpi variants of SPIDER, extend patch --- .../s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb | 40 +++++++++++++++++++ .../s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb | 40 +++++++++++++++++++ .../s/SPIDER/SPIDER-22.10-intel-2015a.eb | 4 +- .../SPIDER-22.10_fix-syntax-ifort.patch | 27 +++++++++++++ 4 files changed, 108 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb new file mode 100644 index 0000000000..051f460b6a --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mpi' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True, 'usempi': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb new file mode 100644 index 0000000000..3638191610 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mt' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True, 'openmp': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DSP_MP" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb index f9744a6899..cf9bac0479 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb @@ -27,9 +27,7 @@ skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' -buildopts += 'FFLAGS="$F90FLAGS -WB -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' -#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DSP_MP -c" LF="$F90FLAGS"' -#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DUSE_MPI -c" LF="$F90FLAGS"' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' modextrapaths = {'PATH': ['spider/bin']} diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch index 3f36cf0b41..57bb1f1a3d 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -69,3 +69,30 @@ $(AR) $(AFLAGS) $(LIB) $*.o - @\rm $*.o +# @\rm $*.o +--- spider/src/four_fq.f.orig 2015-05-21 10:37:01.109541000 +0200 ++++ spider/src/four_fq.f 2015-05-21 10:36:37.703908871 +0200 +@@ -1028,13 +1028,11 @@ + C BUTTERWORTH ELLIPTIC LOWPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + ELSEIF (IOPT == 12) THEN + C BUTTERWORTH ELLIPTIC HIGHPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + + ELSEIF (IOPT == 13) THEN +--- spider/src/lundoc.f.orig 2015-05-21 10:39:00.645329000 +0200 ++++ spider/src/lundoc.f 2015-05-21 10:38:42.870873287 +0200 +@@ -1252,7 +1252,7 @@ + INCLUDE 'CMBLOCK.INC' + + INTEGER :: NDOC,MAXKEYT,MAXREGT,KEYSINUSE,IRTFLG +- LOGICAL :: SAYIT ++ LOGICAL :: SAYIT, ENDFILE + + REAL, POINTER :: IPQ(:) + CHARACTER(LEN=80) :: RECLIN ! ONLY NEEDS START -- GitLab From 0891d0214499d4bdbd11622f1a28da2bd075d69e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:41:25 +0200 Subject: [PATCH 484/992] make FDS patch compatible with recent versions --- easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch index d9c7c2a315..d7106bff9f 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch @@ -1,5 +1,5 @@ ---- makefile (revision 18916) -+++ makefile (working copy) +--- FDS_Compilation/makefile.orig (revision 18916) ++++ FDS_Compilation/makefile (working copy) @@ -29,9 +29,9 @@ # General Purpose Rules -- GitLab From 9519137d051e2f69640db52d87cfa9f5fdd412b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:42:06 +0200 Subject: [PATCH 485/992] {phys}[intel/2015a] FDS r17534 + rr22681 --- .../f/FDS/FDS-r17534-intel-2015a.eb | 32 +++++++++++++++++++ .../f/FDS/FDS-r17534_makefile.patch | 16 ++++++++++ .../f/FDS/FDS-r22681-intel-2015a.eb | 30 +++++++++++++++++ 3 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb new file mode 100644 index 0000000000..2179b3462c --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r17534' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + +unpack_options = '--strip-components=1' + +start_dir = 'FDS_Compilation' + +parallel = 1 + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +modextrapaths = {'PATH': 'FDS_Compilation'} + +sanity_check_paths = { + 'files': ['FDS_Compilation/fds'], + 'dirs': [], +} +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch new file mode 100644 index 0000000000..dea4f7695f --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch @@ -0,0 +1,16 @@ +diff -ru fds-r17534.orig/FDS_Compilation/makefile fds-r17534/FDS_Compilation/makefile +--- fds-r17534.orig/FDS_Compilation/makefile 2013-11-21 17:36:53.000000000 +0100 ++++ fds-r17534/FDS_Compilation/makefile 2015-05-19 13:01:04.892548269 +0200 +@@ -29,9 +29,9 @@ + + # General Purpose Rules + +-no_target: +- @echo \******** You did not specify a make target \******** +- @echo Please read the comments at the top of the makefile ++no_target: FCOMPL = $(F90) ++no_target: setup $(obj_serial) ++ $(FCOMPL) $(FFLAGS) $(LFLAGS) -o fds $(obj_serial) + + setup: + %.o : %.mod diff --git a/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb new file mode 100644 index 0000000000..0b9177003e --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r22681' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['FDS-r18915_makefile.patch'] + +unpack_options = '--strip-components=1' + +start_dir = 'FDS_Compilation' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +modextrapaths = {'PATH': 'FDS_Compilation'} + +sanity_check_paths = { + 'files': ['FDS_Compilation/fds'], + 'dirs': [], +} +moduleclass = 'phys' -- GitLab From 65f9f761750f7e2fd484d4da6704cb5aba44af38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 11:25:23 +0200 Subject: [PATCH 486/992] {vis}[intel/2015a] matplotlib 1.4.3 (w/ Python 3.4.3) --- ...tplotlib-1.4.3-intel-2015a-Python-3.4.3.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb new file mode 100644 index 0000000000..147a7f4db6 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb @@ -0,0 +1,38 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.4.3' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] + +python = "Python" +pythonversion = '3.4.3' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' -- GitLab From acdd3c93de06322ccdce81b8fb9926564d4e9063 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 11:38:09 +0200 Subject: [PATCH 487/992] remove useless comment --- .../m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb | 1 - .../m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb | 1 - .../m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb | 1 - .../m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb | 1 - .../m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb index d97e421867..6a25c33b0c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb @@ -26,7 +26,6 @@ dependencies = [ ('libpng', '1.6.6'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb index 0e33120d40..0397044fea 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb @@ -26,7 +26,6 @@ dependencies = [ ('libpng', '1.6.9'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb index da06531921..8072aaea0f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb @@ -25,7 +25,6 @@ dependencies = [ ('libpng', '1.6.16'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb index 3a24c2da81..25762ccdf7 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb @@ -27,7 +27,6 @@ dependencies = [ ('libpng', '1.6.16'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb index 147a7f4db6..5849d559f7 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb @@ -27,7 +27,6 @@ dependencies = [ ('libpng', '1.6.16'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { -- GitLab From 9880d63fb8810ac68b62411fcfd610b43b6e7830 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 11:49:17 +0200 Subject: [PATCH 488/992] rename to R-bundle, depend on -extra bundle --- ...undle-20150520-intel-2015a-R-3.1.3-devtools.eb} | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/r/{R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb => R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb} (77%) diff --git a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb similarity index 77% rename from easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb rename to easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb index 8cb259acf8..d4a983401d 100644 --- a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -1,10 +1,9 @@ easyblock = 'Bundle' -name = 'R-bundles' +name = 'R-bundle' version = '20150520' -bundlename = 'devtools' rver = '3.1.3' -versionsuffix = '-R-%s-%s' % (rver, bundlename) +versionsuffix = '-R-%s-devtools' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -17,30 +16,25 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('cURL', '7.40.0'), - ('libxml2', '2.9.2'), + ('R-bundle', '20150323-R-%s-extra' % rver), ] -name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], - 'source_tmpl': name_tmpl, + 'source_tmpl': '%(name)s_%(version)s.tar.gz' } # !! order of packages is important !! exts_list = [ - ('XML', '3.98-1.1', ext_options), ('memoise', '0.2.1', ext_options), ('whisker', '0.3-2', ext_options), ('rstudioapi', '0.3.1', ext_options), ('roxygen2', '4.1.1', ext_options), ('git2r', '0.10.1', ext_options), - ('RCurl', '1.95-4.6', ext_options), - ('httr', '0.6.1', ext_options), ('rversions', '1.0.0', ext_options), ('devtools', '1.8.0', ext_options), ] -- GitLab From ed31db7d4b72bef55e57e552e3daa64ead13efac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 12:20:31 +0200 Subject: [PATCH 489/992] rename to R-bundle, move vegan/widgetTools extensions to R easyconfig --- ...dle-20150323-intel-2015a-R-3.1.3-extra.eb} | 10 ++-- .../R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb | 47 ------------------- .../easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 + 3 files changed, 5 insertions(+), 54 deletions(-) rename easybuild/easyconfigs/r/{R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb => R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb} (91%) delete mode 100644 easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb similarity index 91% rename from easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb rename to easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 6cd16e2bf9..108db2e37d 100644 --- a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -1,9 +1,9 @@ easyblock = 'Bundle' -name = 'R-extra' +name = 'R-bundle' version = '20150323' rver = '3.1.3' -versionsuffix = '-R-%s' % rver +versionsuffix = '-R-%s-extra' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -16,8 +16,6 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('Tcl', '8.6.4'), - ('Tk', '8.6.4', '-no-X11'), ('cURL', '7.41.0'), ('libxml2', '2.9.2'), ] @@ -43,11 +41,9 @@ bioconductor_options = { # !! order of packages is important !! exts_list = [ - ('vegan', '2.2-1', ext_options), # requires Tcl/Tk - ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk ('RCurl', '1.95-4.5', ext_options), # requires cURL ('XML', '3.98-1.1', ext_options), # requires libxml2 - # extensions below requires one or more extensions that have an external dependency listed above + # extensions below require one or more extensions that have an external dependency listed above ('picante', '1.6-2', ext_options), ('spacodiR', '0.13.0115', ext_options), ('picante', '1.6-2', ext_options), diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb deleted file mode 100644 index e71e3abf1d..0000000000 --- a/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'Bundle' - -name = 'R-extra' -rver = '3.1.2' -version = '%s-1.0.0' % rver - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -# these are extensions for R -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -dependencies = [ - ('R', rver), - ('GMP', '6.0.0a'), # for gmp -] - -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': name_tmpl, -} -# Bioconductor packages have a different download url -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} - -# !! order of packages is important !! -exts_list = [ - ('gmp', '0.5-12', ext_options), -] - -modextrapaths = {'R_LIBS': ''} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index fefd97519c..b39267177d 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -380,6 +380,8 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk ] moduleclass = 'lang' -- GitLab From e6b4b18c41bf0c69fc9c28be5d0df1c98807a8aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 13:06:12 +0200 Subject: [PATCH 490/992] fix remark --- easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb index 7c9526c34b..4e2d371a71 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb @@ -16,10 +16,9 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] -# dependencies = [('OpenSSL', '1.0.1m')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# dependencies = [('OpenSSL', '1.0.1m')] # configopts = "--with-ssl=$EBROOTOPENSSL" sanity_check_paths = { -- GitLab From f3ffb1ab5ae2797d56b71885ff0dc5992d6bcb27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:01:00 +0200 Subject: [PATCH 491/992] {*}[foss/2015.05] Python 2.7.9 + Boost 1.58.0 + deps --- .../Boost-1.58.0-foss-2015.05-Python-2.7.9.eb | 26 ++++ .../b/bzip2/bzip2-1.0.6-foss-2015.05.eb | 16 +++ .../libreadline-6.3-foss-2015.05.eb | 28 +++++ .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 16 +++ .../p/Python/Python-2.7.9-foss-2015.05.eb | 116 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb | 39 ++++++ .../t/Tcl/Tcl-8.6.3-foss-2015.05.eb | 26 ++++ .../z/zlib/zlib-1.2.8-foss-2015.05.eb | 23 ++++ 8 files changed, 290 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb new file mode 100644 index 0000000000..99e816f731 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb @@ -0,0 +1,26 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_23-09-52 +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb new file mode 100644 index 0000000000..94eb15f42f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb @@ -0,0 +1,16 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-07 +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb new file mode 100644 index 0000000000..09db15bea5 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -0,0 +1,28 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-10-20 +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb new file mode 100644 index 0000000000..46d3cd55d8 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -0,0 +1,16 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-09-34 +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb new file mode 100644 index 0000000000..2e2b6decfa --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -0,0 +1,116 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-50-18 +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb new file mode 100644 index 0000000000..a84b2916e1 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb @@ -0,0 +1,39 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-17-48 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015.05'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb new file mode 100644 index 0000000000..c4895ce18b --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb @@ -0,0 +1,26 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-16-41 +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb new file mode 100644 index 0000000000..6cb32ff060 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb @@ -0,0 +1,23 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-46 +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 5981713451bb61aea69314dfd0e2dd5c45ddea0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:31:09 +0200 Subject: [PATCH 492/992] SPIDER: update patch, use _mp Makefile for -mp/-mpi variants --- .../s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb | 2 +- .../s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb | 2 +- .../SPIDER-22.10_fix-syntax-ifort.patch | 116 +++++++++++++++++- 3 files changed, 112 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb index 051f460b6a..1a775fa535 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -27,7 +27,7 @@ parallel = 1 skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " -buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS"' modextrapaths = {'PATH': ['spider/bin']} diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb index 3638191610..a747562bcb 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb @@ -27,7 +27,7 @@ parallel = 1 skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " -buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DSP_MP" LF="$F90FLAGS"' modextrapaths = {'PATH': ['spider/bin']} diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch index 57bb1f1a3d..957ed589cf 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -1,5 +1,7 @@ +fix syntax issues that trip Intel Fortran compiler (ifort) +author: Kenneth Hoste (HPC-UGent) --- spider/src/copyfromtif.f.orig 2014-11-20 17:31:58.000000000 +0100 -+++ spider/src/copyfromtif.f 2015-05-20 20:18:45.688100002 +0200 ++++ spider/src/copyfromtif.f 2015-05-21 12:04:17.049891641 +0200 @@ -88,7 +88,7 @@ INTEGER(KIND=1), ALLOCATABLE :: I1VALS(:) INTEGER(KIND=4), ALLOCATABLE :: I4VALS(:) @@ -18,15 +20,18 @@ IF (IRTFLG .NE. 0) THEN CALL ERRT(46,'COPYFROMTIF; CVAL...',ICVAL_LEN) -@@ -432,7 +432,7 @@ +@@ -432,9 +432,9 @@ GOTRESU = .TRUE. ELSEIF (ITAG == 306) THEN - CDATE = CVAL(1)(1:22) + CDATE = CVAL(1:22) c IF (DEBUG) WRITE(NOUT,'(2X,A,1X,200A)')'DATE & TIME:', - c & CVAL(1)(1:ICOUNT) +-c & CVAL(1)(1:ICOUNT) ++c & CVAL(1:ICOUNT) GOTDATE = .TRUE. + + ELSE --- spider/src/copypos.f.orig 2015-05-20 21:21:12.693293000 +0200 +++ spider/src/copypos.f 2015-05-20 21:21:37.499077116 +0200 @@ -269,7 +269,7 @@ @@ -85,14 +90,113 @@ ELSEIF (IOPT == 13) THEN ---- spider/src/lundoc.f.orig 2015-05-21 10:39:00.645329000 +0200 -+++ spider/src/lundoc.f 2015-05-21 10:38:42.870873287 +0200 +--- spider/src/spider.f.orig 2015-04-21 15:30:40.000000000 +0200 ++++ spider/src/spider.f 2015-05-21 15:03:36.159704166 +0200 +@@ -195,9 +195,15 @@ + + #ifndef USE_MPI + #ifndef __APPLE__ ++#ifdef SP_IFC ++ isiz1 = kmp_get_stacksize() ++ CALL kmp_set_stacksize(65536) ++ isiz2 = kmp_get_stacksize() ++#else + isiz1 = omp_get_stack_size() + CALL omp_set_stack_size(65536) + isiz2 = omp_get_stack_size() ++#endif + !write(6,*) ' OMP Stack size: ',isiz1,' -->',isiz2 + + #endif +--- spider/src/lundoc.f.orig 2015-03-27 14:08:10.000000000 +0100 ++++ spider/src/lundoc.f 2015-05-21 15:26:30.008871936 +0200 @@ -1252,7 +1252,7 @@ INCLUDE 'CMBLOCK.INC' INTEGER :: NDOC,MAXKEYT,MAXREGT,KEYSINUSE,IRTFLG - LOGICAL :: SAYIT -+ LOGICAL :: SAYIT, ENDFILE ++ LOGICAL :: SAYIT, EOF REAL, POINTER :: IPQ(:) CHARACTER(LEN=80) :: RECLIN ! ONLY NEEDS START +@@ -1319,15 +1319,15 @@ + BACKSPACE(NDOC) ! REREAD LINE + READ(NDOC,*,END=100,IOSTAT=IER) RECLIN + +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ(NDOC,*,END=100,IOSTAT=IER) NKEY,NREGPLINE +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + +- 100 CALL BCAST_MPI('LUNDOCINFO','ENDFILE',ENDFILE,1,'L',ICOMM) ++ 100 CALL BCAST_MPI('LUNDOCINFO','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','IER',IER,1,'I',ICOMM) +- IF (ENDFILE) GOTO 799 ++ IF (EOF) GOTO 799 + + CALL BCAST_MPI('LUNDOCINFO','NKEY',NKEY,1,'I',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','NREGPLINE',NREGPLINE,1, +@@ -1434,7 +1434,7 @@ + + REAL :: PLIST(*) + CHARACTER(LEN=180) :: RECLIN +- LOGICAL :: TILLEND ++ LOGICAL :: TILLEND, EOF, ERRFILE + + CALL SET_MPI(ICOMM,MYPID,MPIERR) ! SETS ICOMM AND MYPID + +@@ -1464,18 +1464,18 @@ + 10 CONTINUE + IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=200) RECLIN + 81 FORMAT(A120) + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + 100 CALL BCAST_MPI('LUNDOCGETCOM','ERRFILE',ERRFILE,1,'L',ICOMM) + IF (ERRFILE) GOTO 998 + +-200 CALL BCAST_MPI('LUNDOCGETCOM','ENDFILE',ENDFILE,1,'L',ICOMM) +- IF (ENDFILE) GOTO 997 ++200 CALL BCAST_MPI('LUNDOCGETCOM','EOF',EOF,1,'L',ICOMM) ++ IF (EOF) GOTO 997 + + CALL BCAST_MPI('LUNDOCGETCOM','RECLIN',RECLIN,180,'C',ICOMM) + +@@ -1580,7 +1580,7 @@ + CHARACTER *120 RECLIN + #ifdef USE_MPI + include 'mpif.h' +- LOGICAL ENDFILE, ERRFILE ++ LOGICAL EOF, ERRFILE + ICOMM = MPI_COMM_WORLD + CALL MPI_COMM_RANK(ICOMM, MYPID, MPIERR) + #else +@@ -1595,15 +1595,15 @@ + #ifdef USE_MPI + 10 IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=100) RECLIN + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + +-100 CALL BCAST_MPI('LUNDOCSAYHDR','ENDFILE',ENDFILE,1,'L',ICOMM) ++100 CALL BCAST_MPI('LUNDOCSAYHDR','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCSAYHDR','ERRFILE',ERRFILE,1,'L',ICOMM) +- IF (ENDFILE .OR. ERRFILE) GOTO 999 ++ IF (EOF .OR. ERRFILE) GOTO 999 + + CALL BCAST_MPI('LUNDOCSAYHDR','RECLIN',RECLIN,120,'C',ICOMM) + #else -- GitLab From 7962d2cba1c7cd60964509de65f0b96a257106ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:35:47 +0200 Subject: [PATCH 493/992] add patch for installing paycheck as Py3 extension --- .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +++ ...aycheck-1.0.2_setup-open-README-utf8.patch | 22 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index c5e5b4ddcb..d79f2b54ad 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -55,6 +55,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], diff --git a/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000..193336def4 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,22 @@ +open README file with utf-8 encoding, to avoid error like: +UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 577: ordinal not in range(128) +author: Kenneth Hoste (HPC-UGent) +--- paycheck-1.0.2/setup.py.orig 2015-05-21 16:09:24.300074046 +0200 ++++ paycheck-1.0.2/setup.py 2015-05-21 16:11:43.503945542 +0200 +@@ -1,6 +1,7 @@ + from distutils.cmd import Command + from distutils.core import setup + ++import codecs + import sys + if sys.version_info >= (3, 0): + try: +@@ -24,7 +25,7 @@ + name = 'paycheck', + version ='1.0.2', + description ='A Python QuickCheck implementation', +- long_description = open("README.txt").read(), ++ long_description = codecs.open("README.txt", encoding='utf-8').read(), + author ='Mark Chadwick', + author_email ='mark.chadwick@gmail.com', + maintainer ='Gregory Crosswhite', -- GitLab From 2294aff5b5e3a456e7598f75d227a55b0454b5c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:38:30 +0200 Subject: [PATCH 494/992] fix remark --- .../b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb | 1 - easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb | 1 - .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb | 1 - easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 1 - easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb | 1 - easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb | 1 - easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb | 1 - 8 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb index 99e816f731..24316a807f 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_23-09-52 name = 'Boost' version = '1.58.0' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb index 94eb15f42f..1c3c8d1851 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-07 name = 'bzip2' version = '1.0.6' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 09db15bea5..c23d9ba711 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-10-20 easyblock = 'ConfigureMake' name = 'libreadline' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index 46d3cd55d8..63b54fa7c4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-09-34 name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 2e2b6decfa..ce15e506fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-50-18 name = 'Python' version = '2.7.9' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb index a84b2916e1..5e77859d07 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-17-48 ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb index c4895ce18b..bd202e0e1b 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-16-41 easyblock = 'ConfigureMake' name = 'Tcl' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb index 6cb32ff060..7668682872 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-46 easyblock = 'ConfigureMake' name = 'zlib' -- GitLab From 9884eda25ed3c0acd92494e121676cf6519bffae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 17:14:31 +0200 Subject: [PATCH 495/992] fix mpi variant of SPIDER --- .../easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb index 1a775fa535..cdcacc4631 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -9,7 +9,7 @@ description = """SPIDER (System for Processing Image Data from Electron microsco an image processing system for electron microscopy.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'static': True, 'usempi': True} +toolchainopts = {'usempi': True} source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] sources = ['spiderweb.%(version)s.tar.gz'] @@ -28,7 +28,7 @@ skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' -buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS"' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS -ldl -lpthread"' modextrapaths = {'PATH': ['spider/bin']} -- GitLab From e3f796267c030c4988e24274c0074483a8681d04 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 21 May 2015 18:23:16 +0200 Subject: [PATCH 496/992] CHARMM for intel/2015a --- .../c/CHARMM/CHARMM-37b2-intel-2015a.eb | 28 ++++++++++ ...CHARMM-37b2_fix-qgas-double-declared.patch | 53 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb new file mode 100644 index 0000000000..155eb5a8ae --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb @@ -0,0 +1,28 @@ +# Authors:: Ward Poelmans + +name = "CHARMM" +version = "37b2" + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "use-xhost-%(version)s.patch", + "main-case-fix-%(version)s.patch", + 'CHARMM-37b2_fix-qgas-double-declared.patch', +] + +# MKL activated automatically when the ictce toolchain is used +build_options = "FULL COLFFT PIPF" + +# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch new file mode 100644 index 0000000000..2c8d36a45f --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch @@ -0,0 +1,53 @@ +reproduction of CHARMM SVN revision 272 (Check-in: http:/charmm.hanyang.ac.kr/6187) +renamed qgas variable in pbeq to qgas1 and updated references in energy +diff -ru c37b2.orig/source/energy/energy.src c37b2/source/energy/energy.src +--- c37b2.orig/source/energy/energy.src 2012-09-29 08:01:42.000000000 +0200 ++++ c37b2/source/energy/energy.src 2015-05-21 16:57:43.951197202 +0200 +@@ -266,7 +266,7 @@ + use param + use pathm + use mpathint, only: qpint, epint !##PATHINT +- use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas,qsmbp,smbp0 !##PBEQ ++ use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas1,qsmbp,smbp0 !##PBEQ + use pbound + use pert + use polarm, only: qpolar, polar1 !##POLAR +@@ -3203,7 +3203,7 @@ + + CALL PBFORCE(NATOM,X,Y,Z,CG,ETERM(PBELEC),ETERM(PBNP), & + DX,DY,DZ,NPBEQ,ecalls,.false. & +- ,QETERM(QMEL),ETERM(QMEL),QGAS & !##SCCDFTB ++ ,QETERM(QMEL),ETERM(QMEL),QGAS1 & !##SCCDFTB + ) + IF (TIMER.GT.1) & + CALL WRTTIM('Poisson Boltzmann Solvation energy times:') +diff -ru c37b2.orig/source/misc/pbeq.src c37b2/source/misc/pbeq.src +--- c37b2.orig/source/misc/pbeq.src 2012-08-08 20:08:30.000000000 +0200 ++++ c37b2/source/misc/pbeq.src 2015-05-21 16:55:47.871787533 +0200 +@@ -19,7 +19,7 @@ + !public :: pbeq0,pbforce,gsbp0,srdist + !QC: export more + public :: pbeq0,pbforce,gsbp0,srdist,m3,dm3,rpowerl2,cosmphi2,sinmphi2,& +- alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas, & ++ alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas1, & + pbeq_iniall,smbp0 + + !variables +@@ -115,7 +115,7 @@ + + ! The following is related to QM/MM implementation of gsbp and pb + ! Xiao_QC_UW0609 +- LOGICAL QPSC,QGAS ++ LOGICAL QPSC,QGAS1 + ##IF SCCDFTB + ! + ! COEFX -----> heap index for COEFX(NTPOL) +@@ -2734,7 +2734,7 @@ + ! XIAO_QC_UW0609 keyword for SCC/PB + MXTPSC = GTRMI(COMLYN,COMLEN,'MXPS',5000) + PSCTOL = GTRMF(COMLYN,COMLEN,'PSTL',1.0D-2) +- QGAS = INDXA(COMLYN,COMLEN,'IGAS').GT.0 ++ QGAS1 = INDXA(COMLYN,COMLEN,'IGAS').GT.0 + ! XIAO_QC_UW0609 add charge dependant radii + QCHDRAD = INDXA(COMLYN,COMLEN,'CHDR').GT.0 + IF (QCHDRAD) THEN -- GitLab From 2642b0323b03578be61758ff225fb8effb98dac6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:09:11 +0200 Subject: [PATCH 497/992] add patch for installing deap as Py3 extension --- .../p/Python/Python-3.4.1-intel-2014b.eb | 6 ++++++ .../p/Python/Python-3.4.1-intel-2015a.eb | 6 ++++++ .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +++ .../deap-1.0.2_setup-open-README-utf8.patch | 17 +++++++++++++++++ 4 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 07f5694321..49334fee76 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -56,6 +56,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -77,6 +80,9 @@ exts_list = [ }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index ba75d726f9..8ddd32db67 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -56,6 +56,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -77,6 +80,9 @@ exts_list = [ }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index d79f2b54ad..a71f6ecf62 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -81,6 +81,9 @@ exts_list = [ ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000..6dece6f5d8 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.2.orig/setup.py 2015-05-12 04:06:49.000000000 +0200 ++++ deap-1.0.2/setup.py 2015-05-21 19:06:03.792820042 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -10,7 +11,7 @@ + from pypandoc import convert + except ImportError: + print("warning: pypandoc module not found, could not convert Markdown to RST") +- read_md = lambda f: open(f, 'r').read() ++ read_md = lambda f: codecs.open(f, encoding='utf-8').read() + else: + read_md = lambda f: convert(f, 'rst') + -- GitLab From 4e5c4223b6c9fe5010909f037306404fef1a24ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:25:22 +0200 Subject: [PATCH 498/992] bump rtracklayer version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 108db2e37d..42f13415a0 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -51,7 +51,7 @@ exts_list = [ ('tkWidgets', '1.44.0', bioconductor_options), ('Mfuzz', '2.26.0', bioconductor_options), ('maSigPro', '1.38.0', bioconductor_options), - ('rtracklayer', '1.26.2', bioconductor_options), + ('rtracklayer', '1.26.3', bioconductor_options), ('BSgenome', '1.34.1', bioconductor_options), ('GEOquery', '2.32.0', bioconductor_options), ('biomaRt', '2.22.0', bioconductor_options), -- GitLab From 929ead97b4a3abcee028477e385cb3c4fe6ab2e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:34:47 +0200 Subject: [PATCH 499/992] bump GenomicFeatures version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 42f13415a0..6fa810b17b 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -62,7 +62,7 @@ exts_list = [ ('GOstats', '2.32.0', bioconductor_options), ('geneplotter', '1.44.0', bioconductor_options), ('DESeq2', '1.6.3', bioconductor_options), - ('GenomicFeatures', '1.18.4', bioconductor_options), + ('GenomicFeatures', '1.18.7', bioconductor_options), ('VariantAnnotation', '1.12.9', bioconductor_options), ('biovizBase', '1.14.1', bioconductor_options), ('OrganismDbi', '1.8.1', bioconductor_options), -- GitLab From 50b099be684215bc154f134486e6a16d856bed98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:47:36 +0200 Subject: [PATCH 500/992] bump KEGGprofile version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 6fa810b17b..732d498ea8 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -78,7 +78,7 @@ exts_list = [ ('Homo.sapiens', '1.1.2', bioconductor_options), ('KEGGgraph', '1.24.0', bioconductor_options), ('KEGGREST', '1.6.4', bioconductor_options), - ('KEGGprofile', '1.8.0', bioconductor_options), + ('KEGGprofile', '1.8.2', bioconductor_options), ('minfi', '1.12.0', bioconductor_options), ('methylumi', '2.12.0', bioconductor_options), ('lumi', '2.18.0', bioconductor_options), -- GitLab From bed4ccdb0fe734f652941f2bf890ae4792000c92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:59:16 +0200 Subject: [PATCH 501/992] bump GViz version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 732d498ea8..a6d53af385 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -82,7 +82,7 @@ exts_list = [ ('minfi', '1.12.0', bioconductor_options), ('methylumi', '2.12.0', bioconductor_options), ('lumi', '2.18.0', bioconductor_options), - ('Gviz', '1.10.10', bioconductor_options), + ('Gviz', '1.10.11', bioconductor_options), ('methyAnalysis', '1.8.0', bioconductor_options), ('pathview', '1.6.0', bioconductor_options), ('SPIA', '2.18.0', bioconductor_options), -- GitLab From 1c264c26a5d5c529eb5cc583f7fb2a4458a7b0dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 21:09:56 +0200 Subject: [PATCH 502/992] move vegan/widgetTools extensions to R foss/2015a easyconfig --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 5d7d661a1f..26e352af95 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -380,6 +380,8 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk ] moduleclass = 'lang' -- GitLab From 9cdee34afd8e5216d72b171cb7b50f3879f4e3fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 22:29:45 +0200 Subject: [PATCH 503/992] include deap v1.0.1 specific patch --- .../p/Python/Python-3.4.1-intel-2014b.eb | 2 +- .../p/Python/Python-3.4.1-intel-2015a.eb | 2 +- .../deap-1.0.1_setup-open-README-utf8.patch | 17 +++++++++++++++++ 3 files changed, 19 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 49334fee76..d3f83f3c59 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -81,7 +81,7 @@ exts_list = [ ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ - 'deap-1.0.2_setup-open-README-utf8.patch', + 'deap-1.0.1_setup-open-README-utf8.patch', ], }), ('decorator', '3.4.0', { diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 8ddd32db67..9f71e6e86f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -81,7 +81,7 @@ exts_list = [ ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ - 'deap-1.0.2_setup-open-README-utf8.patch', + 'deap-1.0.1_setup-open-README-utf8.patch', ], }), ('decorator', '3.4.0', { diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch new file mode 100644 index 0000000000..b7c896999f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.1.orig/setup.py 2014-04-08 15:49:52.000000000 +0200 ++++ deap-1.0.1/setup.py 2015-05-21 22:25:37.345008000 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -11,7 +12,7 @@ + setup(name='deap', + version=deap.__revision__, + description='Distributed Evolutionary Algorithms in Python', +- long_description=open('README.txt').read(), ++ long_description=codecs.open('README.txt', encoding='utf-8').read(), + author='deap Development Team', + author_email='deap-users@googlegroups.com', + url='http://deap.googlecode.com', -- GitLab From 52bf9f7fd6f8803d4ee3f59c3b27f6c5a5ffc0f7 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 21 May 2015 22:35:33 -0400 Subject: [PATCH 504/992] fixed git to include EB perl and path --- .../easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 3 +- .../easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb | 46 +++++++++++++++++++ 2 files changed, 48 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index 48bda49ebe..ceec29fe23 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -29,12 +29,13 @@ preconfigopts = 'make configure && ' # Work around git build system bug. If LIBS contains -lpthread, then configure # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--enable-pthreads='-lpthread'" +configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" dependencies = [ ('cURL', '7.40.0'), ('expat', '2.1.0'), ('gettext', '0.19.4'), + ('Perl', '5.20.1', '-bare'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..d03af57112 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# Authors:: Dmitri Gribenko +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.4.1' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +dependencies = [ + ('cURL', '7.40.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.4'), + ('Perl', '5.20.1', '-bare'), +] + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 54ddbfbfdc33fa68c1ff125bca4e3783e3088d4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 May 2015 10:18:44 +0200 Subject: [PATCH 505/992] fix versionsuffix for extra R-bundle dep --- .../R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb index d4a983401d..5a2b464944 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -16,7 +16,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('R-bundle', '20150323-R-%s-extra' % rver), + ('R-bundle', '20150323', '-R-%s-extra' % rver), ] ext_options = { -- GitLab From d3d92f131d3efdaabfe60b03eb261de2f1730ebf Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 11:24:24 +0200 Subject: [PATCH 506/992] OpenFOAM foss 2015.05 flavour: needed for Centos6 on Haswell --- .../o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb new file mode 100644 index 0000000000..14bd0cffc2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -0,0 +1,58 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_16-18-05 +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432217883, + "build_time": 2389.2, + "install_size": 1888270856, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] -- GitLab From 757910d0c00fcd3f85f4367e5fb29e55b92f4081 Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 12:15:43 +0200 Subject: [PATCH 507/992] adding missing libreadline,SCOTCH,ncurses,flex --- .../f/flex/flex-2.5.39-foss-2015.05.eb | 40 ++++++++++++++ .../libreadline-6.3-foss-2015.05.eb | 53 +++++++++++++++++++ .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 48 +++++++++++++++++ .../s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 40 ++++++++++++++ 4 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb new file mode 100644 index 0000000000..4e10bab03a --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -0,0 +1,40 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-38-14 +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215494, + "build_time": 21.24, + "install_size": 2865429, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb new file mode 100644 index 0000000000..1ad6cea720 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -0,0 +1,53 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-53 +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215473, + "build_time": 17.27, + "install_size": 2395805, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb new file mode 100644 index 0000000000..5ba0974ce8 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -0,0 +1,48 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-36 +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215455, + "build_time": 80.56, + "install_size": 24625439, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb new file mode 100644 index 0000000000..e388e08516 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -0,0 +1,40 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-36-15 +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215375, + "build_time": 70.85, + "install_size": 6501533, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] -- GitLab From a70c7d4b41166f23af8d4a68311170c86dd1594f Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 14:28:00 +0200 Subject: [PATCH 508/992] cleaned comments in flex-2.5.39-foss-2015.05.eb libreadline-6.3-foss-2015.05.eb ncurses-5.9-foss-2015.05.eb OpenFOAM-2.3.1-foss-2015.05.eb SCOTCH-6.0.4-foss-2015.05.eb --- .../f/flex/flex-2.5.39-foss-2015.05.eb | 25 ------------------- .../libreadline-6.3-foss-2015.05.eb | 25 ------------------- .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 25 ------------------- .../o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 25 ------------------- .../s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 25 ------------------- 5 files changed, 125 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb index 4e10bab03a..5f048f3577 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-38-14 name = 'flex' version = '2.5.39' @@ -14,27 +13,3 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] moduleclass = 'lang' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215494, - "build_time": 21.24, - "install_size": 2865429, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 1ad6cea720..93acd649a7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-53 easyblock = 'ConfigureMake' name = 'libreadline' @@ -27,27 +26,3 @@ sanity_check_paths = { moduleclass = 'lib' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215473, - "build_time": 17.27, - "install_size": 2395805, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index 5ba0974ce8..e8393ca7cf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-36 name = 'ncurses' version = '5.9' @@ -22,27 +21,3 @@ configopts = [ moduleclass = 'devel' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215455, - "build_time": 80.56, - "install_size": 24625439, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb index 14bd0cffc2..6f0594b990 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_16-18-05 name = 'OpenFOAM' version = '2.3.1' @@ -32,27 +31,3 @@ builddependencies = [('flex', '2.5.39')] moduleclass = 'cae' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432217883, - "build_time": 2389.2, - "install_size": 1888270856, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb index e388e08516..25db821e80 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-36-15 name = 'SCOTCH' version = '6.0.4' @@ -14,27 +13,3 @@ sources = ['%(namelower)s_%(version)s.tar.gz'] moduleclass = 'math' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215375, - "build_time": 70.85, - "install_size": 6501533, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] -- GitLab From ec29cc694ff50160a089ce904e308b967912d93f Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 15:11:53 +0200 Subject: [PATCH 509/992] a byte cleaner ;) --- easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb | 1 - .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb | 1 - easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 1 - easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb index 5f048f3577..208a02e540 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -12,4 +12,3 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 93acd649a7..c23d9ba711 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index e8393ca7cf..3ab27d3a62 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -20,4 +20,3 @@ configopts = [ ] moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb index 6f0594b990..9e1b2ca02b 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -30,4 +30,3 @@ dependencies = [ builddependencies = [('flex', '2.5.39')] moduleclass = 'cae' - diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb index 25db821e80..f5bdd9828b 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -12,4 +12,3 @@ source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] moduleclass = 'math' - -- GitLab From ae63f1c4b91fbb4ed2ba8a4966887b4f4185c404 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 27 May 2015 09:41:18 +0200 Subject: [PATCH 510/992] Update to Clang 3.6.1 --- .../c/Clang/Clang-3.6.1-GCC-4.9.2.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..15c22eef9c --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.6.1" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '4.9.2'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.0.0'), + ('ISL', '0.14'), +] + +builddependencies = [ + ('CMake', '3.2.1'), + ('Python', '2.7.9', '-bare'), + ('libxml2', '2.9.2'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' -- GitLab From 84c98379f747142ef37eaa45900c867af0f792cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 May 2015 11:04:16 +0200 Subject: [PATCH 511/992] fix GMP 6.0.0a with GCC/4.9.2 --- .../c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb | 25 +++++++++++++++++++ .../easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb | 2 +- 4 files changed, 28 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 445ace0985..40f0a86d6f 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -30,7 +30,7 @@ sources = [ ] dependencies = [ - ('GMP', '6.0.0'), + ('GMP', '6.0.0a'), ('ISL', '0.14'), ] diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb index 08df157950..df7b8848c5 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb @@ -9,7 +9,7 @@ operating on signed integers, rational numbers, and floating point numbers. """ toolchain = {'name': 'GCC', 'version': '4.9.2'} -sources = ["%(namelower)s-%(version)sa.tar.bz2"] +sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb new file mode 100644 index 0000000000..a9855e2029 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.0.0a' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ["%(namelower)s-%(version)s.tar.bz2"] +source_urls = [GNU_SOURCE] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb index 3ba25676db..f6423e5d6e 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['http://isl.gforge.inria.fr/'] sources = [SOURCELOWER_TAR_BZ2] -dependencies = [('GMP', '6.0.0')] +dependencies = [('GMP', '6.0.0a')] sanity_check_paths = { 'files': ['lib/libisl.so', 'lib/libisl.a'], -- GitLab From 6f3f4dcf481be0bd3542527498c81f8346bf0a11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 May 2015 11:30:48 +0200 Subject: [PATCH 512/992] {bio}[dummy] fastqc 0.11.2 + 0.11.3 --- .../easyconfigs/f/fastqc/fastqc-0.11.2.eb | 27 +++++++++++++++++++ .../easyconfigs/f/fastqc/fastqc-0.11.3.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb create mode 100644 easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb new file mode 100644 index 0000000000..9ff730ebed --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.2' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +dependencies = [('Java', '1.7.0_60')] + +postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb new file mode 100644 index 0000000000..c5f20b9165 --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.3' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +dependencies = [('Java', '1.7.0_80')] + +postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' -- GitLab From 0af5491f63d43f506f1382e7c4b8b03394f31089 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 27 May 2015 11:59:09 +0200 Subject: [PATCH 513/992] Change name of gmp version --- easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb index 15c22eef9c..966759d71c 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -30,7 +30,7 @@ sources = [ ] dependencies = [ - ('GMP', '6.0.0'), + ('GMP', '6.0.0a'), ('ISL', '0.14'), ] -- GitLab From ac56b0de721ee0821608eb2d6a84be210e2c4ac1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 May 2015 14:42:17 +0200 Subject: [PATCH 514/992] add fpp + deps as R extensions --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 4 ++++ easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 26e352af95..dee61f1e01 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -382,6 +382,10 @@ exts_list = [ ('Rsubread', '1.16.1', bioconductor_options), ('vegan', '2.2-1', ext_options), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index b39267177d..d50dfde38a 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -382,6 +382,10 @@ exts_list = [ ('Rsubread', '1.16.1', bioconductor_options), ('vegan', '2.2-1', ext_options), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' -- GitLab From e1c84d962128346b1073db16e6f069a8d4acbec6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 11:13:08 +0200 Subject: [PATCH 515/992] include patch to build forecast with Intel compilers --- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch | 9 +++++++++ 2 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index d50dfde38a..56604be04c 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -382,7 +382,7 @@ exts_list = [ ('Rsubread', '1.16.1', bioconductor_options), ('vegan', '2.2-1', ext_options), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk - ('forecast', '6.1', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), ('fma', '2.01', ext_options), ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), diff --git a/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch new file mode 100644 index 0000000000..8582ea93ae --- /dev/null +++ b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch @@ -0,0 +1,9 @@ +ignore warning/error when building with Intel C++ compiler by including -wd308 flag in $CXXFLAGS +author: Kenneth Hoste (HPC-UGent) +--- forecast/src/Makevars.orig 2015-05-12 11:56:10.000000000 +0200 ++++ forecast/src/Makevars 2015-05-28 10:53:13.878100139 +0200 +@@ -1,2 +1,4 @@ + ## Use the R_HOME indirection to support installations of multiple R version + PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From ac6d71a57e7784a9017eb7d5416c05efb0088eca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 12:47:03 +0200 Subject: [PATCH 516/992] {lang}[intel/2015a] Python 2.7.10 --- .../p/Python/Python-2.7.10-intel-2015a.eb | 120 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.10.2-intel-2015a.eb | 40 ++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb new file mode 100644 index 0000000000..e42c4eb9ce --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -0,0 +1,120 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb new file mode 100644 index 0000000000..7f1dc7e31f --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2015a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9a43d2783570dc62fe774b79cd59b0143b8c8e04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 12:49:18 +0200 Subject: [PATCH 517/992] {lang}[foss/2015a] Python 2.7.10 --- .../p/Python/Python-2.7.10-foss-2015a.eb | 120 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.10.2-foss-2015a.eb | 40 ++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb new file mode 100644 index 0000000000..16e9072248 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -0,0 +1,120 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb new file mode 100644 index 0000000000..d5bf2693bd --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From a39319427c8e4fd76769bf875504e4403f245705 Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Thu, 28 May 2015 12:53:15 +0200 Subject: [PATCH 518/992] NEMO easyconfig --- .../easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb new file mode 100644 index 0000000000..cc73946e3e --- /dev/null +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb @@ -0,0 +1,15 @@ +name = 'NEMO' +version = '3.4' + +homepage = 'http://www.nemo-ocean.eu/' +description = 'NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for oceanographic research, operational oceanography seasonal forecast and climate studies.' + +toolchain = {'name': 'ictce','version': '6.1.5'} +toolchainopts = {'opt': False, 'optarch': False} + +with_components = ['OPA_SRC', 'LIM_SRC_3'] +add_keys = ['key_iomput', 'key_mpp_mpi', 'key_dtasal', 'key_dtatem', 'key_tradmp', 'key_lim3', 'key_orca_r1=75'] +del_keys = ['key_lim2', 'key_zdftmx', 'key_orca_r2'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('netCDF-Fortran', '4.2')] -- GitLab From bcdea025bfc604af17e7d4e6b7d2b60796af2937 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:33:19 +0200 Subject: [PATCH 519/992] extend sanity check for SQLite --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb index 7f1dc7e31f..03c9b50fba 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb @@ -33,8 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], } moduleclass = 'devel' -- GitLab From 8ab6b2e829ee34003022ad74349f38f9ffb9ce50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:34:51 +0200 Subject: [PATCH 520/992] extend sanity check for SQLite --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb index d5bf2693bd..fbe46bacc9 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb @@ -33,8 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], } moduleclass = 'devel' -- GitLab From 7d572304650bd03f278d32035f5665c3a7577f22 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:36:46 +0200 Subject: [PATCH 521/992] fix remark --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 16e9072248..08ae2a5f52 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.10' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -- GitLab From 8ec777916625061646218da5cccda84090b7e1ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:37:01 +0200 Subject: [PATCH 522/992] fix remark --- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index e42c4eb9ce..5691adf05e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.10' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -- GitLab From 3882c4aaaed7c4227813b84110b97205f92eb9e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 15:07:40 +0200 Subject: [PATCH 523/992] {phys}[intel/2015a] Geant4 10.01.p01 --- .../c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb | 19 +++++++++++++++ .../g/Geant4/Geant4-10.01.p01-intel-2015a.eb | 24 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb new file mode 100644 index 0000000000..c165bda92e --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.2.0.5' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +separate_build_dir = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb new file mode 100644 index 0000000000..412c19225c --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'Geant4' +version = '10.01.p01' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + ('CLHEP', '2.2.0.5'), +] + +builddependencies = [('CMake', '3.2.2')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' -- GitLab From 9ec1a46de2390d2d455c64ffc2f10606f4d73db5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 15:45:52 +0200 Subject: [PATCH 524/992] add missing CMake build dep --- easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb index c165bda92e..9408c50361 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -14,6 +14,8 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] +builddependencies = [('CMake', '3.2.2')] + separate_build_dir = True moduleclass = 'numlib' -- GitLab From 84c0c0920951a011d2b4514910b746da00c5ebc2 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 29 May 2015 10:55:58 +0200 Subject: [PATCH 525/992] added gcc 4.5.2 --- easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb | 37 ++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb new file mode 100644 index 0000000000..719bc6f315 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb @@ -0,0 +1,37 @@ +name = "GCC" +version = '4.5.2' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, + Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.2.tar.gz', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.8.2.tar.gz', +] + +checksums = [ + 'e31fe695d7235f11fb5a63eafdfbfe88', # gcc-4.5.2.tar.gz + '87e73447afdc2ca5cefd987da865da51', # gmp-5.0.2.tar.gz + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + 'e98267ebd5648a39f881d66797122fb6', # mpc-0.8.2.tar.gz +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +withlto = False + +moduleclass = 'compiler' -- GitLab From 43055375813abdc4dff967afd008353b5646839e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 29 May 2015 11:03:50 +0200 Subject: [PATCH 526/992] Added GCC 4.6.0 --- easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb | 35 ++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb new file mode 100644 index 0000000000..f310421ff2 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb @@ -0,0 +1,35 @@ +name = "GCC" +version = '4.6.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, + Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.4.tar.bz2', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.9.tar.gz', +] + +checksums = [ + '009f59ee0f9c8100c12939140698cf33', # gcc-4.6.0.tar.gz + '50c3edcb7c9438e04377ee9a1a061b79', # gmp-5.0.4.tar.bz2 + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + '0d6acab8d214bd7d1fbbc593e83dd00d', # mpc-0.9.tar.gz +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' -- GitLab From a396d464cc65eba9b7d35613d13be752d63a1e43 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Fri, 29 May 2015 11:48:02 +0200 Subject: [PATCH 527/992] Add hanythingondemand eb files. These could otherwise have been installed w/ --try-software-version --- ...ondemand-2.2.2-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ ...ondemand-2.2.3-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ ...ondemand-2.2.4-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f6063d9ec3 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.2' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..9182229d2c --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.3' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..73433b3081 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.4' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' -- GitLab From 87a8597e5c07722acbe0a06dd001bcf9b04e368d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 May 2015 14:07:44 +0200 Subject: [PATCH 528/992] style fixes in pBWA easyconfig --- .../p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb index 754be559e1..fa5b729bcb 100644 --- a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -13,7 +13,7 @@ name = 'pBWA' version = '0.5.9_1.21009' homepage = 'http://pbwa.sourceforge.net/' -description = """pBWA is a parallel implementation of the popular software BWA. It was developed by modifying the BWA source code with the OpenMPI C library on the SHARCNET. pBWA has been successfully tested on other systems with the most basic OpenMPI installs. pBWA currently implements three commands from BWA: aln, samse, and sampe. pBWA retains and improves upon the multithreading provided by BWA while adding efficient parallelization for the above listed functions. pBWA has shown that its wall-time speedup is bounded only by the size of the parallel system available as pBWA can run on any number of nodes and/or cores simultaneously.""" +description = "pBWA is a parallel implementation of the popular software BWA." toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} @@ -21,18 +21,13 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(name)s_%(version)s.zip'] source_urls = [('http://sourceforge.net/projects/pbwa/files/latest', 'download')] - - -dependencies = [ - ('BWA', '0.7.4'), -] +dependencies = [('BWA', '0.7.4')] files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] sanity_check_paths = { - 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], - 'dirs': ['.'], - + 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], + 'dirs': ['.'], } moduleclass = 'bio' -- GitLab From 3b0eec5db69770911d52947e78b1f89df48c5824 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:00:43 +0200 Subject: [PATCH 529/992] Adding ABySS-1.5.2-goolf-1.4.10 --- .../a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..678a7abd6f --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.5.2' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'usempi': True} + +# eg. http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/1.5.2/'] + +dependencies = [('Boost', '1.53.0')] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c5a863a5e45f620767357721fc87bc880f47759b Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:14:18 +0200 Subject: [PATCH 530/992] Adding BEDTools-2.23.0-goolf-1.4.10 --- .../BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..6dd7cdc664 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.23.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.23.0/bedtools-2.23.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/'] +sources = ['v%(version)s/bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From df353b92cb8dc3d0023eb54ee401cc53622365a5 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:21:00 +0200 Subject: [PATCH 531/992] Comments modifications --- easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb index 678a7abd6f..c055778c8e 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb @@ -2,12 +2,10 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos +# Authors:: Maxime Schmitt , Fotis Georgatos # License:: MIT/GPL # $Id$ # -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## easyblock = 'ConfigureMake' @@ -21,9 +19,8 @@ description = """Assembly By Short Sequences - a de novo, parallel, paired-end s toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} -# eg. http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://github.com/bcgsc/abyss/releases/download/1.5.2/'] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] dependencies = [('Boost', '1.53.0')] -- GitLab From 440afe75a71962fb1c166bc2918f0735000d14de Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:23:50 +0200 Subject: [PATCH 532/992] Modifying comments --- .../easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb index 6dd7cdc664..61147b9331 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -1,4 +1,6 @@ -# Author: Pablo Escobar Lopez +# Author: Maxime Schmitt, University of Luxembourg +# +# Based on the work of: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel -- GitLab From ec543429de043b66a96a3c9df79887ea6bcd0886 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:34:14 +0200 Subject: [PATCH 533/992] Adding Cufflinks-2.2.1-goolf-1.4.10 --- .../Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..9897454369 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['cufflinks-2.2.1.tar.gz'] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c2c18d4e50385d295f2bddd919b09410c0a7887a Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:35:34 +0200 Subject: [PATCH 534/992] Fixing hardcoded version --- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb index 9897454369..3fdf2a0923 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = """Transcript assembly, differential expression, and differential toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['cufflinks-2.2.1.tar.gz'] +sources = ['cufflinks-%(version)s.tar.gz'] source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] dependencies = [ -- GitLab From d09ca49609ada079f83cd2fe185768a3fab2eb23 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:39:37 +0200 Subject: [PATCH 535/992] Fixing source url --- .../easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb index 61147b9331..0c511d17e0 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -17,8 +17,8 @@ description = """The BEDTools utilities allow one to address common genomics tas toolchain = {'name': 'goolf', 'version': '1.4.10'} # https://github.com/arq5x/bedtools2/releases/download/v2.23.0/bedtools-2.23.0.tar.gz -source_urls = ['https://github.com/arq5x/bedtools2/releases/download/'] -sources = ['v%(version)s/bedtools-%(version)s.tar.gz'] +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -- GitLab From ea33e462b738dabf5a7599968dbaef758b8a0b2c Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:51:37 +0200 Subject: [PATCH 536/992] Adding Cython-0.22-goolf-1.4.10-Python-2.7.3.eb --- .../Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..d2b4a22df9 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Cython' +version = '0.22' + +homepage = 'http://pypi.python.org/pypi/Cython/' +description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +cythonsubdir = '-'.join(['Cython', version, 'py'+pythonshortver, 'linux-x86_64.egg']) +cythonlibdir = '/'.join([pylibdir, cythonsubdir]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': ['%s/%%(name)s' % cythonlibdir], +} + +moduleclass = 'lang' -- GitLab From 6915caae459b0f8b730e8b972ee3b98adaa93d9d Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 16:03:08 +0200 Subject: [PATCH 537/992] Adding R-3.2.0-ictce-7.3.5 and its dependencies --- .../libjpeg-turbo-1.4.0-ictce-7.3.5.eb | 24 +++++++++++++++ .../l/libpng/libpng-1.6.17-ictce-7.3.5.eb | 19 ++++++++++++ .../libreadline-6.3-ictce-7.3.5.eb | 29 +++++++++++++++++++ .../n/NASM/NASM-2.11.06-ictce-7.3.5.eb | 19 ++++++++++++ .../n/ncurses/ncurses-5.9-ictce-7.3.5.eb | 15 ++++++++++ .../r/R/R-3.2.0-ictce-7.3.5-bare.eb | 27 +++++++++++++++++ .../z/zlib/zlib-1.2.8-ictce-7.3.5.eb | 22 ++++++++++++++ 7 files changed, 155 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb new file mode 100644 index 0000000000..24b1cf1a07 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb new file mode 100644 index 0000000000..c2db01ab34 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.12' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb new file mode 100644 index 0000000000..34ea8a516d --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +preconfigopts = " LDFLAGS='-ltinfo' " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb new file mode 100644 index 0000000000..d2c0dab761 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb new file mode 100644 index 0000000000..a12e472663 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb @@ -0,0 +1,15 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb new file mode 100644 index 0000000000..cf66631597 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb new file mode 100644 index 0000000000..8254f78ac9 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%s' % version, 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From b2e3c06deb1e415505a3d7d1423a7fc39ca30902 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 16:28:06 +0200 Subject: [PATCH 538/992] Better use of variables --- .../c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index d2b4a22df9..55a97c1d73 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -14,11 +14,9 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -pylibdir = 'lib/python%s/site-packages' % pythonshortver -cythonsubdir = '-'.join(['Cython', version, 'py'+pythonshortver, 'linux-x86_64.egg']) -cythonlibdir = '/'.join([pylibdir, cythonsubdir]) versionsuffix = '-%s-%s' % (python, pythonver) +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +cythonlibdir = 'lib/python%(pythonshortver)s/site-packages/Cython-%(version)s-py%(pythonshortver)s-linux-x86_64.egg' dependencies = [(python, pythonver)] -- GitLab From 10be91757f584afc2df8650f144182daa8338505 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 16:42:55 +0200 Subject: [PATCH 539/992] Fixing name resolutions --- .../c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index 55a97c1d73..08f3c850f6 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -15,8 +15,8 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -cythonlibdir = 'lib/python%(pythonshortver)s/site-packages/Cython-%(version)s-py%(pythonshortver)s-linux-x86_64.egg' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +cythonlibdir = 'lib/python' + pyshortver + '/site-packages/Cython-%(version)s-py' + pyshortver + '-linux-x86_64.egg' dependencies = [(python, pythonver)] -- GitLab From b732ac55bea37f13023094e0bedaca2f0cb8d15c Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 18:25:10 +0200 Subject: [PATCH 540/992] Adding Tcl/Tk dependencies, modifying Java version and fixing version error in libpng --- .../l/libpng/libpng-1.6.17-ictce-7.3.5.eb | 2 +- .../t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb | 24 ++++++++++++++++++ 3 files changed, 50 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb index c2db01ab34..fd641ddebc 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libpng' -version = '1.6.12' +version = '1.6.17' homepage = 'http://www.libpng.org/pub/png/libpng.html' description = "libpng is the official PNG reference library" diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb new file mode 100644 index 0000000000..ab1bbc53d3 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb new file mode 100644 index 0000000000..2363e89fc9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 7739627e35c49cff90c67712ea8af592f3b73509 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 13:44:11 +0200 Subject: [PATCH 541/992] fix typo, remove unneeded configopts --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb index e5ab48448f..25c6d013bc 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -17,8 +17,7 @@ checksums = ['c8b166ec8e65ad1d795d42b889fd772b'] configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' -configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-netcdf-libs="-L$EBROOTLIBXC/lib -lxc" ' -configopts += "fcflags_opt_43_ptgroups='-O0 -g -extend-source'" +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' dependencies = [ ('libxc', '2.2.2'), -- GitLab From 553df5b666baa5856f9ccac51602e323a27b9d78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 14:48:19 +0200 Subject: [PATCH 542/992] {chem}[intel/2015a] ABINIT 7.10.4 --- .../a/ABINIT/ABINIT-7.10.4-intel-2015a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb new file mode 100644 index 0000000000..955b1cd4f1 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.10.4' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bfc76a5f93c3f148c049f57541864e76'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +moduleclass = 'chem' -- GitLab From c67a9ec7774a9c9f488781a504cf51ab135cf180 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 15:05:06 +0200 Subject: [PATCH 543/992] add custom sanity check paths for ABINIT --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb index 955b1cd4f1..24a268901b 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -25,4 +25,9 @@ dependencies = [ ('netCDF-Fortran', '4.4.0'), ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'dirs': ['lib/pkgconfig'], +} + moduleclass = 'chem' -- GitLab From 050fa061b42d083907090abebe3df8017142b871 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 15:05:23 +0200 Subject: [PATCH 544/992] add custom sanity check paths for ABINIT --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb index 25c6d013bc..51c5aef3d9 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -25,4 +25,9 @@ dependencies = [ ('netCDF-Fortran', '4.4.0'), ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'dirs': ['lib/pkgconfig'], +} + moduleclass = 'chem' -- GitLab From 57168333ad91183825fc00bbb34cc0322bcbdccd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 20:31:13 +0200 Subject: [PATCH 545/992] fix typo --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb index 51c5aef3d9..97bc886c26 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } -- GitLab From 0f48dfa2c9bc9443825325f101a985d9e306ae5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 20:31:35 +0200 Subject: [PATCH 546/992] fix typo --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb index 24a268901b..7561f6f45c 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } -- GitLab From 6857cd98a5c3de64c6a53265cd490c4da464b4a9 Mon Sep 17 00:00:00 2001 From: Ingrid Barcena Roig Date: Mon, 1 Jun 2015 10:37:53 +0200 Subject: [PATCH 547/992] Gromacs 5.0.5-intel2015a easycofig --- .../GROMACS-5.0.5-intel-2015a-hybrid.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..09ed0e7dc1 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.5' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.1.0'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.57.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From 73db870ee8050759cb01d991f35404ca5d37887f Mon Sep 17 00:00:00 2001 From: Ingrid Barcena Roig Date: Mon, 1 Jun 2015 17:35:50 +0200 Subject: [PATCH 548/992] Gromacs 5.0.5-intel2015a easycofig --- .../easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb index 09ed0e7dc1..c7e0273a3e 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb @@ -25,10 +25,10 @@ source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('CMake', '3.1.0'), + ('CMake', '3.2.2'), ('libxml2', '2.9.2') ] -dependencies = [('Boost', '1.57.0', '-Python-2.7.9')] +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] moduleclass = 'bio' -- GitLab From bd81df67d7ee4ce73bb19e2869d24077f280b9fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Jun 2015 18:59:22 +0200 Subject: [PATCH 549/992] fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs --- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb | 3 +-- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb | 3 +-- .../QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb | 3 +-- .../QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb | 3 +-- .../QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb | 3 +-- .../QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb | 3 +-- 10 files changed, 10 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb index 9409f95fc2..89cf3c3778 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb index 4a03ccc94b..ec449db284 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb index d97dae5c5d..476628bcd5 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb index d7fb61f42c..e0dbe69249 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb index 04f547b28a..0b54c5912d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb index 479e526fb3..c6b5e835da 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb index 1b9a405ed8..a5a5338771 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb index 5740815aa1..9007ee9bb7 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb index bf87cf39af..f4b21d4cab 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb index a341ebad38..aa0ea72322 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ -- GitLab From be2f94d281c7560934c72b997676ac1b65dceac7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 09:42:46 +0200 Subject: [PATCH 550/992] fix remark --- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb | 2 +- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb | 2 +- .../QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb index 89cf3c3778..d000d6ec7f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb index ec449db284..a34afc570a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb index 476628bcd5..5ef2e6d1b1 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb index e0dbe69249..1e036026da 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb index 0b54c5912d..464f263647 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb index c6b5e835da..cd0fac60cb 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb index a5a5338771..9533b73dfd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb index 9007ee9bb7..b3212736f0 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb index f4b21d4cab..ae347ad0bd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb index aa0ea72322..2a054ef2d3 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] -- GitLab From f0b78c2b17b0111a3369d9987b94c32d70b0156f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 10:29:40 +0200 Subject: [PATCH 551/992] {vis}[intel/2015a] libXScrnSaver 1.2.2 + libXft 2.3.2 --- .../fontconfig-2.11.93-intel-2015a.eb | 22 ++++++++++++ .../k/kbproto/kbproto-1.0.7-intel-2015a.eb | 19 +++++++++++ .../libXScrnSaver-1.2.2-intel-2015a.eb | 24 +++++++++++++ .../libXft-2.3.2-intel-2015a-libX11-1.6.3.eb | 34 +++++++++++++++++++ .../libXrender-0.9.9-intel-2015a.eb | 28 +++++++++++++++ .../renderproto-0.11-intel-2015a.eb | 20 +++++++++++ 6 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb new file mode 100644 index 0000000000..77235f32a1 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.93' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb new file mode 100644 index 0000000000..62923f260f --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb new file mode 100644 index 0000000000..0889930509 --- /dev/null +++ b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXScrnSaver' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Screen Saver extension client library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXext', '1.3.3') +] + +sanity_check_paths = { + 'files': ['lib/libXss.a', 'lib/libXss.so', 'include/X11/extensions/scrnsaver.h'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000..65123b2fae --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.6'), + ('renderproto', '0.11'), +] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver + +dependencies = [ + ('libX11', libx11ver, '-Python-2.7.9'), + ('libXrender', '0.9.9'), + ('freetype', '2.5.5'), + ('fontconfig', '2.11.93'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb new file mode 100644 index 0000000000..393ccdfa93 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('renderproto', '0.11'), +] + +dependencies = [ + ('kbproto', '1.0.7'), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb new file mode 100644 index 0000000000..b1d4936121 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs' : [], +} + +moduleclass = 'devel' -- GitLab From b559f80695feb569bbee527ed6d64fae204ced1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 10:48:47 +0200 Subject: [PATCH 552/992] include Tk as dependency in Python 2.7.9 easyconfigs --- .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 1 + .../p/Python/Python-2.7.9-foss-2015.05.eb | 1 + .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 1 + .../p/Python/Python-2.7.9-foss-2015a.eb | 1 + .../Python/Python-2.7.9-gompi-1.5.16-bare.eb | 1 + .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 1 + .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 1 + .../p/Python/Python-2.7.9-intel-2015a.eb | 1 + .../easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb | 25 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-foss-2015.05.eb | 25 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb | 25 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb | 24 ++++++++++++++++++ .../t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb | 24 ++++++++++++++++++ .../t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb | 24 ++++++++++++++++++ .../t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb | 24 ++++++++++++++++++ 16 files changed, 204 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index 3974b6e842..e9840cb7eb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index ce15e506fc..0fa5529cb0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 669c54c38d..5eed3b0154 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 3273aa0399..1ff5189a78 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index e206b78e22..2f9941dfab 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -17,6 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 9a1f9af5fc..536743d8c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index d2c02867a9..499a28228b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 95f4d38205..71a627c500 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb new file mode 100644 index 0000000000..fcf9fcc830 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb new file mode 100644 index 0000000000..a933eab557 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb new file mode 100644 index 0000000000..099c4a95f4 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb new file mode 100644 index 0000000000..150f56cf00 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb new file mode 100644 index 0000000000..3530d74282 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb new file mode 100644 index 0000000000..337e722e7b --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb new file mode 100644 index 0000000000..58076d4e59 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb new file mode 100644 index 0000000000..6b858f2d9d --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 04bfc4827d82c852f29b1360dc93240de08a80e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:19:37 +0200 Subject: [PATCH 553/992] include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works --- .../p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 10 +++++++++- 6 files changed, 54 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb index 2ec3cb1dc8..5c84059a20 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index fdb44db0d0..39d6b11c34 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb index 09917d5025..1e9572eb83 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index bb0be0ac85..466ad2cc0c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb index 10c6659238..3fafaaa920 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index 3950c920d4..5a66cda69a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' -- GitLab From 7e6618a5642325d9039922026ba539a5ff50fce7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:27:09 +0200 Subject: [PATCH 554/992] use Tk 8.6.3 rather than Tk 8.6.4 as dep in Python 2.7.9 easyconfigs --- .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015.05.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015a.eb | 2 +- .../Python/Python-2.7.9-gompi-1.5.16-bare.eb | 2 +- .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 2 +- .../p/Python/Python-2.7.9-intel-2015a.eb | 2 +- .../easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb | 25 ------------------- .../t/Tcl/Tcl-8.6.4-foss-2015.05.eb | 25 ------------------- .../t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb | 25 ------------------- .../t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb | 25 ------------------- ...no-X11.eb => Tk-8.6.3-GCC-4.9.2-no-X11.eb} | 2 +- ...X11.eb => Tk-8.6.3-foss-2015.05-no-X11.eb} | 2 +- .../t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb | 24 ++++++++++++++++++ ...X11.eb => Tk-8.6.3-gompi-1.5.16-no-X11.eb} | 2 +- ...X11.eb => Tk-8.6.3-goolf-1.5.14-no-X11.eb} | 2 +- 17 files changed, 36 insertions(+), 112 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-GCC-4.9.2-no-X11.eb => Tk-8.6.3-GCC-4.9.2-no-X11.eb} (97%) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-foss-2015.05-no-X11.eb => Tk-8.6.3-foss-2015.05-no-X11.eb} (97%) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-gompi-1.5.16-no-X11.eb => Tk-8.6.3-gompi-1.5.16-no-X11.eb} (97%) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-goolf-1.5.14-no-X11.eb => Tk-8.6.3-goolf-1.5.14-no-X11.eb} (97%) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index e9840cb7eb..7f438347a5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 0fa5529cb0..d0661c356d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 5eed3b0154..dc26dc666b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 1ff5189a78..cc0e90d0e3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index 2f9941dfab..ad2c37f79a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -17,7 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 536743d8c5..bb0fac1650 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index 499a28228b..d6a4eb1b3c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 71a627c500..ed4d77fc45 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb deleted file mode 100644 index fcf9fcc830..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'GCC', 'version': '4.9.2'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb deleted file mode 100644 index a933eab557..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'foss', 'version': '2015.05'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb deleted file mode 100644 index 099c4a95f4..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'gompi', 'version': '1.5.16'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb deleted file mode 100644 index 150f56cf00..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'goolf', 'version': '1.5.14'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb index 3530d74282..602101704a 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb index 337e722e7b..8ff29d34a2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb new file mode 100644 index 0000000000..c34f24fd99 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb index 58076d4e59..a292e06eb8 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb index 6b858f2d9d..cd4da6afb6 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' -- GitLab From 37f24102612713bb52c192907e11889040d172e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:34:16 +0200 Subject: [PATCH 555/992] kbproto is just a build dep --- .../easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb index 778cd1670c..cea866f2b7 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb index fe8ecdca33..80e0f6ea24 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb index 393ccdfa93..52e06388f3 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.7'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.7'), ('libX11', '1.6.3', '-Python-2.7.9'), ] -- GitLab From 6dbc6268d466d2a34aaad21e94b9b5168f25406c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:43:49 +0200 Subject: [PATCH 556/992] add missing Tk 8.6.3 intel/2015a easyconfig --- .../t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb new file mode 100644 index 0000000000..d841e7bd84 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From a8b8cd6eeb84d5902bdc13b762b65f95a992f383 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 16:10:50 +0200 Subject: [PATCH 557/992] {data}[intel/2015a] HDF5 1.8.15 --- .../h/HDF5/HDF5-1.8.15-intel-2015a.eb | 27 ++++++ .../h/HDF5/HDF5-1.8.15_configure_intel.patch | 95 +++++++++++++++++++ 2 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb new file mode 100644 index 0000000000..e820f700da --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.15' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-%(version)s_configure_intel.patch', + 'configure_libtool.patch', +] + +configopts = "--enable-gpfs" +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch new file mode 100644 index 0000000000..b74e70593e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch @@ -0,0 +1,95 @@ +--- hdf5-1.8.15/configure.orig 2015-05-01 20:56:59.000000000 +0200 ++++ hdf5-1.8.15/configure 2015-06-02 15:04:26.757168623 +0200 +@@ -5190,7 +5190,7 @@ + ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $ac_fcflags_srcext conftest.$ac_ext $LIBS >&5' + ac_compiler_gnu=$ac_cv_fc_compiler_gnu + if test -n "$ac_tool_prefix"; then +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. + set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +@@ -5234,7 +5234,7 @@ + fi + if test -z "$FC"; then + ac_ct_FC=$FC +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -11993,7 +11993,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc*| ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-fPIC' + lt_prog_compiler_static='-static' +@@ -12629,11 +12629,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec= +@@ -13115,7 +13115,7 @@ + link_all_deplibs=yes + allow_undefined_flag="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -16113,7 +16113,7 @@ + link_all_deplibs_CXX=yes + allow_undefined_flag_CXX="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -19024,7 +19024,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc* | ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl_FC='-Wl,' + lt_prog_compiler_pic_FC='-fPIC' + lt_prog_compiler_static_FC='-static' +@@ -19645,11 +19645,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec_FC='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec_FC= +@@ -20103,7 +20103,7 @@ + link_all_deplibs_FC=yes + allow_undefined_flag_FC="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then -- GitLab From d52f65e1ad073313821ba555c1cfa7d83f6e580c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 16:42:09 +0200 Subject: [PATCH 558/992] drop gpfs versionsuffix and use no longer existing --enable-gpfs configopt for recent HDF5 versions --- ...1.8.14-intel-2015a-gpfs.eb => HDF5-1.8.14-intel-2015a.eb} | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb | 1 - ...-2.7.9-gpfs.eb => h5py-2.5.0-intel-2015a-Python-2.7.9.eb} | 5 ++--- easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb | 2 +- 5 files changed, 4 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.8.14-intel-2015a-gpfs.eb => HDF5-1.8.14-intel-2015a.eb} (92%) rename easybuild/easyconfigs/h/h5py/{h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb => h5py-2.5.0-intel-2015a-Python-2.7.9.eb} (88%) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb similarity index 92% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb index 081c94297d..2b7af38374 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb @@ -1,6 +1,5 @@ name = 'HDF5' version = '1.8.14' -versionsuffix = '-gpfs' homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of @@ -17,7 +16,6 @@ patches = [ 'configure_libtool.patch', ] -configopts = "--enable-gpfs" buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb index e820f700da..9b028b25b8 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -16,7 +16,6 @@ patches = [ 'configure_libtool.patch', ] -configopts = "--enable-gpfs" buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb similarity index 88% rename from easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb rename to easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index d6f4de7c55..665337345c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -17,12 +17,11 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.9' pyshortver = '.'.join(pyver.split('.')[0:2]) -hdf5suff = '-gpfs' -versionsuffix = '-%s-%s%s' % (python, pyver, hdf5suff) +versionsuffix = '-%s-%s%s' % (python, pyver) dependencies = [ (python, pyver), - ('HDF5', '1.8.14', hdf5suff), + ('HDF5', '1.8.14'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb index 822615186c..baee3155cf 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb @@ -20,7 +20,7 @@ patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.4'), - ('HDF5', '1.8.14', '-gpfs'), + ('HDF5', '1.8.14'), ('libctl', '3.2.2'), ('GSL', '1.16'), ('FFTW', '3.3.4') diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb index bd7faf3909..0f9bc0fa5f 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '2.7.9'), # should have a working sqlite, and provide numpy ('freetype', '2.5.5'), ('LibTIFF', '4.0.4beta'), - ('HDF5', '1.8.14', '-gpfs'), + ('HDF5', '1.8.14'), ('libjpeg-turbo', '1.4.0'), ('FFTW', '3.3.4'), ('SQLite', '3.8.8.1'), # must match SQLite used by Python -- GitLab From d7c8a53fc9087c0fdaf8c5abffe9330540ad3a50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 16:55:12 +0200 Subject: [PATCH 559/992] fix typo --- .../easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index 665337345c..44ec9edf7c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -17,7 +17,7 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.9' pyshortver = '.'.join(pyver.split('.')[0:2]) -versionsuffix = '-%s-%s%s' % (python, pyver) +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), -- GitLab From 06f663105c14f3491674941f2cc4101acf93f6c8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 16:57:17 +0200 Subject: [PATCH 560/992] cURL added as dependency --- easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb index cdf98f1940..1931792850 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -21,6 +21,7 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), ('netCDF', '4.3.2') + ('cURL', '7.37.1') ] moduleclass = 'math' -- GitLab From b1d2fff1ebdf73d28a511d6c7d29417d4349507c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:12:20 +0200 Subject: [PATCH 561/992] Added external matplotlib dependency and source changed to PYPI --- .../HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb | 7 +++- ...tplotlib-1.3.1-intel-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ 2 files changed, 42 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb index 1f11e79748..b9dd51cded 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' @@ -17,7 +17,10 @@ pyshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver -dependencies = [(python, pythonver)] +dependencies = [ + (python, pythonver), + ('matplotlib', '1.3.1'), +] sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..91d3707f42 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.3.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.8' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.3'), + ('libpng', '1.6.12'), +] + +# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' -- GitLab From a8a944bb018cc966c76271071b87249621bba31b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:19:13 +0200 Subject: [PATCH 562/992] toolchain corrected in matplotlib --- .../m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb index 91d3707f42..765f86a131 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb @@ -8,7 +8,7 @@ description = """matplotlib is a python 2D plotting library which produces publi hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" -toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 6bfc7b9b575209908f2ae661dc2180271d60c315 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:25:50 +0200 Subject: [PATCH 563/992] using GMP-GCC-4.9.2 --- easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb index 77009b52a1..aef6e26abf 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] -dependencies = [('GMP', '6.0.0a')] +dependencies = [('GMP', '6.0.0a', '', ('GCC', '4.9.2'))] configopts = "--with-gmp" -- GitLab From 4e6379444e094b0540033f5c84af4a56c197d32b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:43:43 +0200 Subject: [PATCH 564/992] versionsuffix added for matplotlib dependency --- .../h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb index b9dd51cded..0118dd4b32 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -19,7 +19,7 @@ eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver dependencies = [ (python, pythonver), - ('matplotlib', '1.3.1'), + ('matplotlib', '1.3.1', versionsuffix), ] sanity_check_paths = { -- GitLab From a81ac042848534cce51d17a81c942d378ca67459 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 08:26:53 +0200 Subject: [PATCH 565/992] include checksum + switch to manual download in JUBE easyconfig --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index 0044a1ec87..e0a6db9551 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -1,7 +1,7 @@ -easyblock = "VersionIndependentPythonPackage" +easyblock = 'VersionIndependentPythonPackage' -name = "JUBE" -version = "2.0.3" +name = 'JUBE' +version = '2.0.3' homepage = "http://www.fz-juelich.de/jsc/jube" description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, @@ -9,8 +9,9 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ["http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s"] +# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s sources = [SOURCELOWER_TAR_GZ] +checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] options = {'modulename': 'jube2'} -- GitLab From b2b544310020b5da5d34d5b5baf35ba59b686d5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 08:27:08 +0200 Subject: [PATCH 566/992] add easyconfigs for JUBE 2.0.4 an 2.0.5 --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 23 ++++++++++++++++++++++ easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 23 ++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb new file mode 100644 index 0000000000..dc76af6562 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.4' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96a7946d38d678b25ba4bbd539482a14'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb new file mode 100644 index 0000000000..ea72eb6be6 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.5' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f506e9f39898af3d7456890ba219ab90'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 662aeb0bdca15c55e38160a0249872c94e802cf9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 08:34:47 +0200 Subject: [PATCH 567/992] commas corrected --- .../easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb index 1931792850..47cf63ba0e 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -20,8 +20,8 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), - ('netCDF', '4.3.2') - ('cURL', '7.37.1') + ('netCDF', '4.3.2'), + ('cURL', '7.37.1'), ] moduleclass = 'math' -- GitLab From cf66efb4e2461ba170c389924bbb7928fcabadb6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 08:37:53 +0200 Subject: [PATCH 568/992] SOURCELOWER -> SOURCE --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index e0a6db9551..ffff4a9c2e 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -10,7 +10,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} # requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] options = {'modulename': 'jube2'} diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index dc76af6562..373d162154 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -10,7 +10,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} # requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = ['96a7946d38d678b25ba4bbd539482a14'] options = {'modulename': 'jube2'} diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index ea72eb6be6..ebf3c0a914 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -10,7 +10,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} # requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = ['f506e9f39898af3d7456890ba219ab90'] options = {'modulename': 'jube2'} -- GitLab From 4454fbfccee430c04edbba49254539a3b724388a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 09:01:02 +0200 Subject: [PATCH 569/992] Both packages use dependency GMP-GCC-4.9.2 --- easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb index 00491cc9ba..270390d86d 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] -dependencies = [('GMP', '6.0.0a')] +dependencies = [('GMP', '6.0.0a', '', ('GCC', '4.9.2'))] configopts = "--with-gmp" -- GitLab From d3824d539f8d45ed0b2537a3631a4e75dceac622 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 09:11:24 +0200 Subject: [PATCH 570/992] md5schecksum added --- easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb index 2698ca5e91..920ee4c4fa 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -25,5 +25,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/'] sources = ['%(namelower)s_%(version)s_linux_64.run'] +checksums = [('md5', '90b1b8f77313600cc294d9271741f4da')] moduleclass = 'system' -- GitLab From 0c716a66441012c284d71f3bc0a81b70147ac387 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 10:26:11 +0300 Subject: [PATCH 571/992] Fixed config --- .../easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb index 99d44c6862..79d3f53e5a 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -1,11 +1,12 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou # License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'MATIO' version = '1.5.2' @@ -16,10 +17,8 @@ description = """matio is an C library for reading and writing Matlab MAT files. toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] - -dependencies = [('zlib','1.2.7'), -] +dependencies = [('zlib','1.2.7')] moduleclass = 'lib' -- GitLab From a5f4228dc8bc378fe248f5d9b86c1dd5a6c64750 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 10:43:11 +0300 Subject: [PATCH 572/992] Fixes in easyconfig --- .../DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb index d3ec591256..2734b69ecf 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -7,19 +7,20 @@ # $Id$ # ## - easyblock = "PythonPackage" name = 'DendroPy' version = '3.12.0' homepage = 'https://pypi.python.org/pypi/DendroPy/' -description = """A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. -""" +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://pypi.python.org/packages/source/D/DendroPy/'] -sources = ['%s-%s.tar.gz' % (name, version)] +sources = [SOURCE_TAR_GZ] python = "Python" pythonversion = '2.7.3' @@ -30,7 +31,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py','bin/sumtrees.py','bin/strict_consensus_merge.py'], + 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py', + 'bin/sumtrees.py','bin/strict_consensus_merge.py'], 'dirs': [], } -- GitLab From b684e5971fa21996893a2a3be3e4d2d3a292f2c6 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 09:52:28 +0200 Subject: [PATCH 573/992] renamed to MuTect and updated download url --- ...t-1.1.4-Java-1.7.0_76.eb => MuTect-1.1.4-Java-1.7.0_76.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/m/MuTect/{muTect-1.1.4-Java-1.7.0_76.eb => MuTect-1.1.4-Java-1.7.0_76.eb} (94%) diff --git a/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb similarity index 94% rename from easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb rename to easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb index ee2805d464..2a8458e2e5 100644 --- a/easybuild/easyconfigs/m/MuTect/muTect-1.1.4-Java-1.7.0_76.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb @@ -5,7 +5,7 @@ easyblock = 'Tarball' -name = 'muTect' +name = 'MuTect' version = '1.1.4' homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' @@ -16,7 +16,7 @@ description = """ MuTect is a method developed at the Broad Institute for the re toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] -sources = ['%(name)s-%(version)s-bin.zip'] +sources = ['muTect-%(version)s-bin.zip'] java = 'Java' javaver = '1.7.0_76' -- GitLab From 3027f180c35a32b5289a5ed0b669c5d95e5a9915 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 09:58:57 +0200 Subject: [PATCH 574/992] add source_urls using download.php?file= --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index ffff4a9c2e..2803f111f1 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index 373d162154..31b888866e 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['96a7946d38d678b25ba4bbd539482a14'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index ebf3c0a914..4313248d99 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['f506e9f39898af3d7456890ba219ab90'] -- GitLab From 283908c4c27cc74b3b44d5d4499ee76aaffd8826 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 10:02:36 +0200 Subject: [PATCH 575/992] fix typo --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index 2803f111f1..903be570eb 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index 31b888866e..545b5785ea 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['96a7946d38d678b25ba4bbd539482a14'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index 4313248d99..b270f53d57 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['f506e9f39898af3d7456890ba219ab90'] -- GitLab From 884bc004100e2103387e49640296ab011510c3e4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 3 Jun 2015 10:12:07 +0200 Subject: [PATCH 576/992] use autotools --- easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index c3b27fffcb..43293cbe1d 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [('Autoconf', '2.69')] +builddependencies = [('Autotools', '20150205', '', ('GCC', '4.9.2'))] patches = ['cairo-1.12.18-pthread-check.patch'] -- GitLab From 1df688fd2a9832a2b272060ed4e14c35680005ae Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 3 Jun 2015 10:18:49 +0200 Subject: [PATCH 577/992] correct version --- easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index 43293cbe1d..c4afd6154b 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [('Autotools', '20150205', '', ('GCC', '4.9.2'))] +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] patches = ['cairo-1.12.18-pthread-check.patch'] -- GitLab From 03a20f0bcdfefa678a34e5a201eda032b944b7b4 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 11:33:48 +0300 Subject: [PATCH 578/992] Changes in config file --- .../b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index d749578a18..beb147df02 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -6,30 +6,26 @@ # License:: MIT/GPL # ## - easyblock = "Tarball" name = 'Bismark' version = '0.10.1' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/bismark/' -description = """A tool to map bisulfite converted sequence reads and determine cytosine methylation states""" +description = """A tool to map bisulfite converted sequence reads and +determine cytosine methylation states""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["www.bioinformatics.babraham.ac.uk/projects/bismark/"] sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] - -dependencies = [ - ('Bowtie2', '2.0.2'), -] +dependencies = [('Bowtie2', '2.0.2')] sanity_check_paths = { - 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", + "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], 'dirs': [], } -modextrapaths = {'PATH': ''} - moduleclass = 'bio' -- GitLab From 91aa792c2defe803b961a11f29f81ca5540bf6a8 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 11:45:23 +0300 Subject: [PATCH 579/992] removing ABINIT files; bismark branch --- .../a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb | 38 ------------------- .../ABINIT-7.4.3-x86_64_linux_gnu4.5.eb | 32 ---------------- .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 29 -------------- 3 files changed, 99 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb delete mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb delete mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb deleted file mode 100644 index a3fe29c410..0000000000 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## - -name = 'ABINIT' -version = '7.4.3' - -homepage = 'http://www.abinit.org/' -description = """Abinit is a plane wave pseudopotential code for doing - condensed phase electronic structure calculations using DFT.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 -sources = ['%s-%s.tar.gz' % (name.lower(), version)] -source_urls = ['http://ftp.abinit.org/'] - -configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' -configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' -configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' -configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' - -dependencies = [ - ('netCDF', '4.1.3'), - ('ETSF_IO', '1.0.4'), -] - -sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb deleted file mode 100644 index fb4d81965f..0000000000 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb +++ /dev/null @@ -1,32 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## - -easyblock = "Tarball" - -name = 'ABINIT' -version = '7.4.3' -versionsuffix = '-x86_64_linux_gnu4.5' - -altversions = ['7.0.3', '7.0.4', '7.0.5'] - -homepage = 'http://www.abinit.org/' -description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 -sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] -source_urls = ['http://ftp.abinit.org/'] - -sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb deleted file mode 100644 index 350da2d908..0000000000 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb +++ /dev/null @@ -1,29 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## - -name = 'ETSF_IO' -version = '1.0.4' - -homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' -description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] - -configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" - -dependencies = [ ('netCDF', '4.1.3') ] - -sanity_check_paths = { - 'files': ["bin/etsf_io"], - 'dirs': [] - } - -moduleclass = 'chem' -- GitLab From 27381d2c985988915b21e13302101816a61ed6a3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 10:47:17 +0200 Subject: [PATCH 580/992] using separate python module --- ...uitscape-4.0.5-intel-2014b-Python-2.7.8.eb | 1 + .../PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb | 31 +++++++++++++++++++ .../p/Python/Python-2.7.8-intel-2014b.eb | 31 ++++++++++--------- 3 files changed, 48 insertions(+), 15 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb index a07b1584dc..b2653a8675 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb @@ -23,6 +23,7 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), + ('PyAMG', '2.2.1', versionsuffix), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..0bbb1b820f --- /dev/null +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'PyAMG' +version = '2.2.1' + +homepage = 'http://pyamg.org' +description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.8' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +options = {'modulename': 'pyamg'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pyamg' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 76a6bcb647..787f5ecab1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -22,19 +22,22 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + # order is important! # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['https://mpi4py.googlecode.com/files/'], + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -63,9 +66,12 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], @@ -81,20 +87,15 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), ('pyparsing', '2.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), - ('matplotlib', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], - }), - ('pyamg', '2.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyamg/'], - }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] - moduleclass = 'lang' -- GitLab From e486daf541a839a09ff57dd7ee0eb0f0ee462421 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 10:56:59 +0200 Subject: [PATCH 581/992] trial to remove Python modifications --- .../p/Python/Python-2.7.8-intel-2014b.eb | 28 ++++++++----------- 1 file changed, 12 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 787f5ecab1..fc03cf9418 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -22,22 +22,19 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - # order is important! # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +46,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://mpi4py.googlecode.com/files/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -66,12 +63,9 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), - ('six', '1.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], @@ -87,15 +81,17 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), ('pyparsing', '2.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), + ('matplotlib', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' -- GitLab From 8550a555814b6331d8193536a75e6ac41672181c Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 12:05:35 +0300 Subject: [PATCH 582/992] Fixing source_url --- easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index beb147df02..337980614f 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -17,7 +17,7 @@ determine cytosine methylation states""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ["www.bioinformatics.babraham.ac.uk/projects/bismark/"] +source_urls = ["http://www.bioinformatics.babraham.ac.uk/projects/bismark/"] sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] dependencies = [('Bowtie2', '2.0.2')] -- GitLab From e6e6f48a7a4693953e8bb38614d4b52bc3950877 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 11:18:02 +0200 Subject: [PATCH 583/992] synced with current develop, foss/2015a version updated --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb index 8319de8066..e42de69332 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb @@ -12,7 +12,10 @@ toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] -- GitLab From 3a8ac4416f6863c307ee4d585d749cc355853ab0 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 12:18:14 +0300 Subject: [PATCH 584/992] Fixed configs according to comments --- ...BINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb} | 23 +++++++++++-------- .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 21 +++++++++++------ 2 files changed, 28 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/a/ABINIT/{ABINIT-7.4.3-goolf-1.4.10.eb => ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb} (59%) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb similarity index 59% rename from easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb rename to easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb index c1d2b559d8..4d319523ac 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb @@ -1,35 +1,40 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2014 The Cyprus Institute +# Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou +# License:: MIT/GPL # ## +easyblock = "ConfigureMake" name = 'ABINIT' version = '7.4.3' +versionsuffix = '-ETSF_IO-1.0.4' homepage = 'http://www.abinit.org/' -description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' -configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' dependencies = [ - ('netCDF', '4.1.3'), - ('ETSF_IO', '1.0.4'), + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), ] sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } + 'files': ["bin/abinit"], + 'dirs': [] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb index 7e1b945d47..f270612d5f 100644 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -1,27 +1,34 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2014 The Cyprus Institute +# Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou +# License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'ETSF_IO' version = '1.0.4' homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' -description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ +description = """A library of F90 routines to read/write the ETSF file +format has been written. It is called ETSF_IO and available under LGPL. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] +source_urls = ['http://www.etsf.eu/system/files'] +sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" +configopts = "--with-netcdf-prefix=$EBROOTNETCDF " +configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' " +configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include'" dependencies = [ ('netCDF', '4.1.3') ] sanity_check_paths = { - 'files': ["bin/etsf_io"], - 'dirs': [] - } + 'files': ["bin/etsf_io"], + 'dirs': [] +} +moduleclass = 'lib' -- GitLab From 5c634f7678d0ae2e66f3b90f1b384d507c190e40 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 11:23:58 +0200 Subject: [PATCH 585/992] sourceLOWER added --- .../p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb index 0bbb1b820f..360297f0ce 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb @@ -8,8 +8,8 @@ description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCELOWER] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.8' -- GitLab From 00f7b94da182e20d1ed4b8d80ef20e768459e095 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 11:32:41 +0200 Subject: [PATCH 586/992] PYPI_LOWER_SOURCE fixed --- .../easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb index 360297f0ce..44847179db 100644 --- a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb @@ -8,7 +8,7 @@ description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = [PYPI_SOURCELOWER] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' -- GitLab From bfe7601591b4c8c24c965692748dcae63dd63a5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 11:52:30 +0200 Subject: [PATCH 587/992] include MD5sum for CUDA 6.0.37 source file --- easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb index 0ebf372eeb..76cb0b94f9 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -24,5 +24,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # http://developer.download.nvidia.com/compute/cuda/6_0/rel/installers/cuda_6.0.37_linux_64.run source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/rel/installers/'] sources = ['%(namelower)s_%(version)s_linux_64.run'] +checksums = ['22f50793b6704fe987983302fa7d1707'] moduleclass = 'system' -- GitLab From ee063ccdefc5305aeb3e36a04ff0dd03f5f0a6ee Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Wed, 3 Jun 2015 12:03:40 +0200 Subject: [PATCH 588/992] - Pango-1.36.7-intel-2014b.eb : added missing dependency ('libXft', '2.3.2') because of sanity check --- easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb index eba092fa74..1de69091f3 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb @@ -22,6 +22,7 @@ dependencies = [ ('GLib', '2.40.0'), ('HarfBuzz', '0.9.35'), ('GObject-Introspection', '1.42.0'), + ('libXft', '2.3.2'), ] builddependencies = [ -- GitLab From fc0c5c7a197088ae823d7c208dc8b4c420db129f Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Wed, 3 Jun 2015 12:08:11 +0200 Subject: [PATCH 589/992] - Qt-4.8.6-intel-2014b.eb : updated source_urls --- easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb index 1c0c56d935..b87b87bd72 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb @@ -7,8 +7,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -- GitLab From ed27a09ec26e06e4a07bd257e6f3705ffb427c89 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 26 Mar 2014 15:52:55 +0100 Subject: [PATCH 590/992] fixed ECore easyconfigs and dependencies, since it simply doesn't work with a openmpi built with gcc --- .../e/ECore/ECore-1.5.2-clusterapps.eb | 4 +- easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb | 3 +- .../h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb | 17 ++++++++ .../o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 39 +++++++++++++++++++ 4 files changed, 59 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb index 526f2442cd..6bfb37241d 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb @@ -13,8 +13,8 @@ sources = ['%s-%s%s.tgz' % (name.lower(), version, versionsuffix)] patches = ['ecore-license-var.patch'] -comp = ('GCC', '4.6.3') -dependencies = [('OpenMPI', '1.4.5', '-no-OFED', comp)] +# needs to be 1.4.x, because it's linked with the libmpi_cxx.so.0 +dependencies = [('OpenMPI', '1.4.5', '-ictce-5.5.0')] sanity_check_paths = { 'files': ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['absperm', 'FormationFactor', 'nmr', diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb index 382a1b327e..dd16f0a9f1 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb @@ -12,8 +12,7 @@ sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -comp = ('GCC', '4.6.3') -dependencies = [('OpenMPI', '1.4.5', '-no-OFED', comp)] +dependencies = [('OpenMPI', '1.4.5', 'ictce', '5.5.0')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb new file mode 100644 index 0000000000..884dc745a7 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb @@ -0,0 +1,17 @@ +name = 'hwloc' +version = "1.7.2" + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb new file mode 100644 index 0000000000..f65c7d844b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -0,0 +1,39 @@ +name = 'OpenMPI' +version = "1.4.5" + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +builddependencies = [ + ('Automake', '1.14'), + ('Autoconf', '2.69'), +] + +dependencies = [('hwloc', '1.7.2')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-openib +if OS_NAME in ['debian', 'ubuntu']: + osdependencies = ['libibverbs-dev'] +else: + # OK for OS_NAME == redhat, fedora, RHEL, SL, centos + osdependencies = ['libibverbs-devel'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", + "mpi_f77", "mpi_f90", + "mpi", "open-pal", "open-rte"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From 45e3c80bc1eac0c18c835964f6ea8b2af9a523d3 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 3 Apr 2014 11:02:16 +0200 Subject: [PATCH 591/992] fixed wrong suffix --- easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb index dd16f0a9f1..ce44a8981d 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -dependencies = [('OpenMPI', '1.4.5', 'ictce', '5.5.0')] +dependencies = [('OpenMPI', '1.4.5', 'ictce-5.5.0')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ -- GitLab From 19981e5adc20b2a545d5b1612d1d3ba7dd8c6dac Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 3 Apr 2014 11:10:44 +0200 Subject: [PATCH 592/992] another typo fix in toolchain version --- easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb index ce44a8981d..5e6f6b0b1c 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -dependencies = [('OpenMPI', '1.4.5', 'ictce-5.5.0')] +dependencies = [('OpenMPI', '1.4.5', '-ictce-5.5.0')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ -- GitLab From 171f98c6ee423731fce8b2d7468181131b0b28e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 12:25:01 +0200 Subject: [PATCH 593/992] fix ncurses patch for v5.9-20130406 --- .../n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 2 +- .../ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 2 +- .../ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 2 +- .../ncurses-5.9-20130406_configure_darwin.patch | 11 +++++++++++ 8 files changed, 18 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 6d40fe65a5..634fda5b4d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 7d2df71a8f..4f21474dcf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index a971bf0cc9..a71c6aab72 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 360335ba07..f2a6bbb76a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 021bbd904f..5ef3e822ad 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 439c4ca406..96cc600747 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 1fcb38e69b..a1409a10e6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch new file mode 100644 index 0000000000..067ec128f9 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch @@ -0,0 +1,11 @@ +--- ncurses-5.9-20130406/configure.orig 2013-04-07 00:09:21.000000000 +0200 ++++ ncurses-5.9-20130406/configure 2015-06-03 12:20:33.765043843 +0200 +@@ -5587,7 +5587,7 @@ + chmod +x mk_shared_lib.sh + ;; + darwin*) #(vi +- cf_try_cflags="no-cpp-precomp" ++ #cf_try_cflags="no-cpp-precomp" + CC_SHARED_OPTS="-dynamic" + MK_SHARED_LIB='${CC} ${CFLAGS} -dynamiclib -install_name ${libdir}/`basename $@` -compatibility_version ${ABI_VERSION} -current_version ${ABI_VERSION} -o $@' + test "$cf_cv_shlib_version" = auto && cf_cv_shlib_version=abi -- GitLab From e8952f17f155a4029f7ed8fbe4e11854e62cd493 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 24 Sep 2014 13:25:46 +0200 Subject: [PATCH 594/992] added paraview for intel-2014b --- .../g/GLib/GLib-2.41.2-intel-2014b.eb | 18 +++++++++++++++ .../p/Paraview/Paraview-4.1.0-intel-2014b.eb | 22 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb create mode 100644 easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb new file mode 100644 index 0000000000..23fc05daec --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -0,0 +1,18 @@ +name = 'GLib' +version = '2.41.2' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" +toolchain = {'name': 'intel', 'version': '2014b'} # tweaked by EasyBuild (was: {'name': 'foss', 'version': '2014b'}) +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.1'), + ('gettext', '0.19.2'), +] +builddependencies = [('Python', '2.7.8')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb b/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb new file mode 100644 index 0000000000..2f704c2b24 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'CMakeMake' + +name = 'Paraview' +version = '4.1.0' + +homepage = "http://www.paraview.org" +description = "Paraview is a scientific parallel visualizer" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s-source.tar.gz"] + +dependencies = [('Qt','4.8.6')] + +builddependencies = [('CMake', '3.0.0')] + +separate_build_dir = True + +moduleclass = 'vis' -- GitLab From 910656a9c7a0b3cbcb1684970a8a06c0ba81ba07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 12:35:05 +0200 Subject: [PATCH 595/992] use %(version)s rather than hardcoding 5.9 in ncurses patch specs --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 4 +--- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 2 +- 33 files changed, 33 insertions(+), 35 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index 399dc72d43..37a2fff35a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index bcf8a1dcfa..96e1f45472 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index d967731cf4..5dd295c39e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 9608f82f81..3071876ad2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -8,15 +8,13 @@ description = """The Ncurses (new curses) library is a free software emulation o and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" -patches = ['ncurses-5.9_configure_darwin.patch'] - toolchain = {'name': 'GCC', 'version': '4.8.2'} toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 6bf4c2b332..c5e4c7e93d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 6313c884fc..5125329966 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index 727175a0e9..7278bb4ccf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index 26e6ab54bf..cff4af273d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index c993267096..b529181479 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 38361f94f7..aaa5b2bd78 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index b057182b0c..f8ee92d094 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index d67bdf2770..9936cdbc6c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 169534ccd8..b5428d27b0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 7e1f5ce19f..21128a21c5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 2df180dac8..fa8d19afbb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index c31fdc08ca..cdf8cdb5ce 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index bfba6b87fe..36b5053e62 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 76b20bd13a..292cec33e2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index 1cb1b2fa6b..0b4bbba9ad 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index cf54b65a18..b5099d8795 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 7ee6110e8d..94e44f7817 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 5753a19c6f..b1c1a88d75 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index 7466ea8529..fed58a89dd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 2df3b61306..bf996a362f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index 0d8611a193..671b5796ac 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index ce62d53ca0..61118f9005 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index 017c395992..278cc8d64a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index b6a67863ad..38c7d07988 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index edb943229c..9fa751952c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 4912fd41da..24097805bc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 389a334b0b..115d1bd981 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index ab5729d6df..e4351873f4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 1a23dd3813..529b47259f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-5.9_configure_darwin.patch'] +patches = ['ncurses-%(version)s_configure_darwin.patch'] configopts = [ # default build -- GitLab From d9b6f0b5ffa86dbf02905755cf4b574476c43ece Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 12:41:11 +0200 Subject: [PATCH 596/992] sync ncurses easyconfigs --- .../n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 22 +++++++++++++++---- .../n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 22 +++++++++++++++---- .../n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 22 +++++++++++++++---- .../n/ncurses/ncurses-5.9-GCC-4.8.4.eb | 19 ++++++++++++++++ .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 20 ++++++++++++++--- .../n/ncurses/ncurses-5.9-gompi-1.5.16.eb | 21 ++++++++++++++++++ .../n/ncurses/ncurses-5.9-goolf-1.7.20.eb | 21 ++++++++++++++++++ .../n/ncurses/ncurses-5.9-intel-2014.06.eb | 21 ++++++++++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9.eb | 21 ++++++++++++++++++ 9 files changed, 174 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb index 23ac2489aa..0683b0f7a3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -7,16 +9,28 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb index 95c1010bbc..6cb29748e3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -7,16 +9,28 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb index af63de1cff..96517f4a7a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -7,16 +9,28 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb index 946a1c5338..a769a56170 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb @@ -14,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index 3ab27d3a62..37d7e04809 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,11 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb index 9f6619baca..e272a823d6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb index a62ac8f668..9a1708ba34 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb index e1045e7b9f..d67fc45cbf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 6ab79de61f..dd70b0800a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' -- GitLab From dab59113ad43a5ee0a40449487138c7a24ec2e0e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 12:45:01 +0200 Subject: [PATCH 597/992] fixed remarks --- .../easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index 16f1a1e3ae..8acfc38319 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -11,15 +11,15 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +source_urls = ['SOURCEFORGE_SOURCE'] -dependencies = [ - ('Bison', '3.0.2'), - ('flex', '2.5.39'), +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), ] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ngmakeidx', 'ngmultidec', 'ngnutmeg', 'ngproc2mod', 'ngsconvert', 'ngspice']], - 'dirs': [], + 'dirs': [], } moduleclass = 'cae' -- GitLab From 5264f8e1bf6be28dffd88d0ccfa62c3e9a107dbb Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 12:50:00 +0200 Subject: [PATCH 598/992] Explicitly add EasyBlock='ConfigureMake' --- easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 2 ++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb index 884dc745a7..c914d40121 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +EasyBlock = 'ConfigureMake' + name = 'hwloc' version = "1.7.2" @@ -10,7 +12,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide information about modern computing hardware so as to exploit it accordingly and efficiently.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} - + source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index f65c7d844b..5b5a80e895 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +EasyBlock = 'ConfigureMake' + name = 'OpenMPI' version = "1.4.5" -- GitLab From 32c3812fe39fd9171d66a5d0b13330aec2cde43f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 12:54:03 +0200 Subject: [PATCH 599/992] Explicitly add EasyBlock='ConfigureMake' --- easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index 23fc05daec..f3e83d90ac 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -1,3 +1,5 @@ +EasyBlock = 'ConfigureMake' + name = 'GLib' version = '2.41.2' -- GitLab From bc620c3f35a0b7373e13feb920ff66560f942ba6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 12:58:49 +0200 Subject: [PATCH 600/992] enable 'shared' tcopt in ncurses Cray easyconfigs --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb index 0683b0f7a3..6b7bb1c347 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb index 6cb29748e3..01680ab5b7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb index 96517f4a7a..6f00fdbd51 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -- GitLab From 6dfc9321176f7a2132b7018132623a9bdccd9d9f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:16:07 +0200 Subject: [PATCH 601/992] Explicitly add EasyBlock='ConfigureMake' --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index 8acfc38319..942515bb81 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -1,3 +1,5 @@ +EasyBlock = 'ConfigureMake' + name = 'ngspice' version = '26' -- GitLab From dcdc87c8a8fb10c283eb2d3d6dae7ee37f5ab3ff Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:18:42 +0200 Subject: [PATCH 602/992] Explicitly add easyblock='ConfigureMake' --- easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb index c914d40121..1f891126fd 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb @@ -1,4 +1,4 @@ -EasyBlock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'hwloc' version = "1.7.2" diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index 5b5a80e895..585ea11236 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -1,4 +1,4 @@ -EasyBlock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'OpenMPI' version = "1.4.5" -- GitLab From 5a247ac0ebf67be5b8a49c97280a9143f94a26a8 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:20:19 +0200 Subject: [PATCH 603/992] Explicitly add easyblock='ConfigureMake' --- easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index f3e83d90ac..cec860f2de 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -1,4 +1,4 @@ -EasyBlock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GLib' version = '2.41.2' -- GitLab From b74af28326bb0c4850578ab7a4cec1b59bb73de1 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:28:46 +0200 Subject: [PATCH 604/992] fixed tecplot ec name 6 remarks --- .../t/tecplot360ex/tecplot-360ex.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb new file mode 100644 index 0000000000..08531bb3f3 --- /dev/null +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'tecplot360ex' +version = 'linux64' + +homepage = 'http://www.tecplot.com/' +description = """ + Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, + and communicate your results with professional images and animations. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://www.tecplot.com/my/product-releases/ +installername = '%(name)s_%(version)s.sh' +sources = [installername] + +sanity_check_paths = { + 'files': ['bin/tec360'], + 'dirs': [] +} +install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) + +moduleclass = 'vis' -- GitLab From 20ca4139b6f20a4317666ed82ff4f48c91ccb19e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:32:05 +0200 Subject: [PATCH 605/992] fixed remarks --- .../easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb | 13 +++++++------ .../easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 10 ++++++++-- 2 files changed, 15 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb index 175efc7a74..4ed102f04a 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -2,14 +2,15 @@ # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'tabix' version = '0.2.6' homepage = 'http://samtools.sourceforge.net' -description = """ Generic indexer for TAB-delimited genome position files """ +description = """ Generic indexer for TAB-delimited genome position files """ toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -21,12 +22,12 @@ dependencies = [('zlib', '1.2.8')] files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), (["tabix.1"], "man/man1"), - "example.gtf.gz", + "example.gtf.gz", "example.gtf.gz.tbi", - "NEWS", + "NEWS", "ChangeLog" -] -makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +] +makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index 2f4bddea4e..8e12dc4f34 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -1,4 +1,10 @@ -easyblock='MakeCp' +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University + +easyblock = 'MakeCp' name = 'tabix' version = '0.2.6' @@ -20,7 +26,7 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], -- GitLab From 1c74b575fa8e499af1f7057ff847af3c6736b844 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:33:03 +0200 Subject: [PATCH 606/992] makeopts -> buildopts --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb index 4ed102f04a..808db8594a 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -27,7 +27,7 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index 8e12dc4f34..f364f9fafd 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -1,4 +1,5 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +pts # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel @@ -26,7 +27,7 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -makeopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], -- GitLab From a43ea9539a862566d62ba036b152a5e05d6a6662 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 14:33:35 +0300 Subject: [PATCH 607/992] Fixes after review --- .../easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb | 10 +++++++--- easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb | 10 +++++++--- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb index 4661417502..2060e3874c 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -1,18 +1,19 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou # License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'PROJ' version = '4.8.0' homepage = 'http://trac.osgeo.org/proj/' description = """Program proj is a standard Unix filter function which converts - geographic longitude and latitude coordinates into cartesian coordinates""" +geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -21,6 +22,9 @@ source_urls = ['http://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], 'dirs': [], } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb index 589656723f..427477bf96 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -1,18 +1,19 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou # License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'PROJ' version = '4.8.0' homepage = 'http://trac.osgeo.org/proj/' description = """Program proj is a standard Unix filter function which converts - geographic longitude and latitude coordinates into cartesian coordinates""" +geographic longitude and latitude coordinates into cartesian coordinates""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -21,6 +22,9 @@ source_urls = ['http://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/cs2cs','bin/geod','bin/invgeod','bin/invproj','bin/nad2bin','bin/proj'], + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], 'dirs': [], } + +moduleclass = 'lib' -- GitLab From 301b11ffb83d864cb71f2bc4cd08cef67fc62e91 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:33:58 +0200 Subject: [PATCH 608/992] Explicitly add easyblock='ConfigureMake' --- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index 942515bb81..d22d8136b3 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -1,4 +1,4 @@ -EasyBlock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'ngspice' version = '26' -- GitLab From dfd5a4cd444ffd206e1007be32d805e8e3b16282 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:43:29 +0200 Subject: [PATCH 609/992] fixed osdependencies for OpenMPI --- .../easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index 585ea11236..c793f86806 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -24,11 +24,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + -- GitLab From f9fdbd6119398a606825ce7b0637be5e32e43120 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 14:44:08 +0300 Subject: [PATCH 610/992] Style Fixes --- .../Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb | 16 +++++++--------- .../Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb | 17 +++++++---------- 2 files changed, 14 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb index 8308ab148a..28482a1b30 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb @@ -4,8 +4,8 @@ name = 'Theano' version = '0.6.0' homepage = 'http://deeplearning.net/software/theano' -description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions -involving multi-dimensional arrays efficiently.""" +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -17,14 +17,12 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -dependencies = [ - (python, pythonver), - ] +dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/theano-cache', - 'lib/python%s/site-packages/%s-%s-py%s.egg' % (pythonshortver, name, version, pythonshortver)], - 'dirs': [] - } + 'files': ['bin/theano-cache', 'lib/python%s/site-packages/%s-%s-py%s.egg' + % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb index 1e72223824..e95fac6936 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb @@ -4,9 +4,8 @@ name = 'Theano' version = '0.6.0' homepage = 'http://deeplearning.net/software/theano' -description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions - involving multi-dimensional arrays efficiently.""" - +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} @@ -18,14 +17,12 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -dependencies = [ - (python, pythonver), - ] +dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/theano-cache', - 'lib/python%s/site-packages/%s-%s-py%s.egg' % (pythonshortver, name, version, pythonshortver)], - 'dirs': [] - } + 'files': ['bin/theano-cache', 'lib/python%s/site-packages/%s-%s-py%s.egg' + % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] +} moduleclass = 'math' -- GitLab From 2730bfd14d00b9cb9bb465eceb7570cf6af1a77d Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 13:51:17 +0200 Subject: [PATCH 611/992] Revert "Delete imkl-10.3.12.361.eb" This reverts commit 7f2076dcc517dcac3b51742cc86ddb20cc274adf. --- .../easyconfigs/i/imkl/imkl-10.3.12.361.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb new file mode 100644 index 0000000000..dfb97e3568 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -0,0 +1,29 @@ +name = 'imkl' +version = '10.3.12.361' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] + +# deps for interface build +dependencies = [ + ('icc', '2011.13.367'), + ('ifort', '2011.13.367'), + ('impi', '4.1.0.027'), +] + +dontcreateinstalldir = 'True' + +interfaces = True + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'numlib' -- GitLab From d0ecabf99cf121127f2095ccb938843ad648fa67 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 13:52:03 +0200 Subject: [PATCH 612/992] Revert "Delete impi-4.1.0.027.eb" This reverts commit 83ac4560b153fbadb3103c3cfb7b7efdb3691444. --- .../easyconfigs/i/impi/impi-4.1.0.027.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb new file mode 100644 index 0000000000..d074eeb0ea --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '4.1.0.027' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['/share/src/Intel/2011/l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' -- GitLab From 29c3488210050842cfab67fb62b7f859c789e6c5 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 12 Aug 2014 10:42:48 +0200 Subject: [PATCH 613/992] Don't run the Bloom tests for Jellyfish, they can randomly fail --- .../easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb index 595bb566df..e874c05030 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -runtest = "check" +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" sanity_check_paths = { 'files': ['bin/jellyfish'], -- GitLab From 59f614145445bd94c9dc18e8b420ef491e8a387e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:57:55 +0200 Subject: [PATCH 614/992] removed bad easyconfig --- .../t/tecplot360ex/tecplot360ex.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb deleted file mode 100644 index 08d437e5b8..0000000000 --- a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'Binary' - -name = 'tecplot360ex' -version = 'linux64' - -homepage = 'http://www.tecplot.com/' -description = """ - Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, - and communicate your results with professional images and animations. -""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# fi. http://www.tecplot.com/my/product-releases/ -installername = '%(name)s_%(version)s.sh' -sources = [installername] - -sanity_check_paths = { - 'files': ['bin/tec360'], - 'dirs': [] -} -install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) -moduleclass = 'vis' - -- GitLab From a80d2cd20acb2b51dde642f34c292967a9f8017e Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 14:01:24 +0200 Subject: [PATCH 615/992] Fixed intermittent modifications after revert --- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb | 8 +++++--- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index dfb97e3568..0db4c8f64f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -9,12 +9,14 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['/share/src/Intel/2011/l_mkl_%(version)s_intel64.tgz'] +sources = ['l_mkl_%(version)s.tgz'] + +compver = '2011.13.367' # deps for interface build dependencies = [ - ('icc', '2011.13.367'), - ('ifort', '2011.13.367'), + ('icc', compver), + ('ifort', compver), ('impi', '4.1.0.027'), ] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index d074eeb0ea..839fe8f604 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['/share/src/Intel/2011/l_mpi_p_%(version)s.tgz'] +sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' -- GitLab From 273386ca814a34da61bd54d5860de661d4a91f4b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 14:09:27 +0200 Subject: [PATCH 616/992] Use %(version)s as suggested --- easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb index e4a2454e0e..0b93b9c580 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -16,7 +16,7 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" -sources = ['binutils-%s.tar.bz2' % version] +sources = ['binutils-%(version)s.tar.bz2'] source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.5.14'} -- GitLab From 21a0a26dae34726e73e5e9330a6fde4f04eae2f4 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 14:21:31 +0200 Subject: [PATCH 617/992] Updated easyconfigs --- .../b/binutils/binutils-2.22-goolf-1.5.14.eb | 8 +++++--- .../easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb | 10 +++++++--- .../easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb | 2 ++ .../easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb | 2 ++ easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb | 2 ++ 5 files changed, 18 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb index 0b93b9c580..1922cb5d12 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -10,18 +10,20 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## +easyblock = 'ConfigureMake' + name = 'binutils' version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" -sources = ['binutils-%(version)s.tar.bz2'] -source_urls = [GNU_SOURCE] - toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} +sources = ['binutils-%(version)s.tar.bz2'] +source_urls = [GNU_SOURCE] + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb index 3628401ad4..b4f0251684 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -3,6 +3,7 @@ # License:: New BSD # ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -17,13 +18,16 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'goolf', 'version': '1.5.14'} -# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] dependencies = [('Qt', '4.8.4')] -configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support is has difficulties handling +# parallel builds. +configopts = "--without-java-reader" sanity_check_paths = { 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb index c2bd8f4970..9e66f41f61 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -3,6 +3,8 @@ # License:: New BSD # ## +easyblock = 'ConfigureMake' + name = "OPARI2" version = "1.1.2" diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb index f1dcf6fbfe..d485c2eb57 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## +easyblock = 'ConfigureMake' + name = 'PAPI' version = '5.2.0' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb index 1933e4066b..85a3447e47 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb @@ -3,6 +3,8 @@ # License:: New BSD # ## +easyblock = 'ConfigureMake' + name = "PDT" version = "3.20" -- GitLab From c5df41c24c550dd9ddb29ba8cd61e3f1ad615442 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Jun 2015 14:24:22 +0200 Subject: [PATCH 618/992] Cosmetics --- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb index 9e66f41f61..34e2fdbcea 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -3,6 +3,7 @@ # License:: New BSD # ## + easyblock = 'ConfigureMake' name = "OPARI2" diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb index e0a03c63d3..60c9ce8691 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb @@ -6,6 +6,7 @@ # This work is based from experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "OTF2" diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb index 85a3447e47..bb1e979e80 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb @@ -3,6 +3,7 @@ # License:: New BSD # ## + easyblock = 'ConfigureMake' name = "PDT" diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb index 196dc0e191..137bacee9c 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -3,6 +3,7 @@ # License:: New BSD # # make sure we don't fall back to the ConfigureMake easyblock + easyblock = 'EB_Score_minus_P' name = "Score-P" -- GitLab From 01fe2f370f5b7e04aac75a9f2f30317be57732a3 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 3 Jun 2015 08:42:36 -0400 Subject: [PATCH 619/992] adding the easyblock for ConfigureMake --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb index bbe68cc575..b307dca6af 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = 'BCFtools' version = '1.1' -- GitLab From 5eec0de784d331e48c3c0b17d232813a4357e777 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 15:06:14 +0200 Subject: [PATCH 620/992] remove outdated comment --- easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb index c9ba2ffbaf..cbf18980bc 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb @@ -24,7 +24,6 @@ description = """PAPI provides the tool designer and application engineer with a toolchain = {'name': 'foss', 'version': '2015a'} -# Example download URL, for reference: http://icl.cs.utk.edu/projects/papi/downloads/papi-5.0.0.tar.gz source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] sources = [SOURCELOWER_TAR_GZ] -- GitLab From c9dc018ba771899d25cc843d23bda87e3e67e52d Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Wed, 3 Jun 2015 15:31:15 +0200 Subject: [PATCH 621/992] - Perl-5.20.0-intel-2014b.eb : added some extensions (needed for SOBA) --- .../p/Perl/Perl-5.20.0-intel-2014b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb index 197f8c762a..afa1c420a1 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb @@ -812,6 +812,59 @@ exts_list = [ 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB/'], }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAVIDO/'], + }), + ('Text::CSV', '1.32', { + 'source_tmpl': 'Text-CSV-1.32.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/'], + }), + ('Number::Format', '1.73', { + 'source_tmpl': 'Number-Format-1.73.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/W/WR/WRW/'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DARREN/'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AN/ANDYA/'], + }), + ('Text::Table', '1.15', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/S/'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RU/RUZ/'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Test::Pod', '1.50', { + 'source_tmpl': 'Test-Pod-1.50.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DW/DWHEELER/'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], + }), + ] moduleclass = 'lang' -- GitLab From cad86d34fcb09fa830f307891fd476103dc03db5 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:33:29 +0200 Subject: [PATCH 622/992] fixed sanity check and message on load --- easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb index 2a8458e2e5..afe163b841 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb @@ -25,12 +25,12 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] sanity_check_paths = { - 'files': ["%(name)s-%(version)s.jar"], + 'files': ["muTect-%(version)s.jar"], 'dirs': [], } modloadmsg = """ -to execute: java -jar \\$EBROOTMUTECT/%(name)s-%(version)s.jar +to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar """ moduleclass = 'bio' -- GitLab From cac43dea05551c515ca2c0b8207bf3f53d22d274 Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Wed, 3 Jun 2015 15:35:49 +0200 Subject: [PATCH 623/992] - GraphViz-2.18-intel-2014b-Perl-5.20.0.eb : new Perl interface to Graphviz --- .../GraphViz-2.18-intel-2014b-Perl-5.20.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb diff --git a/easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000..a7968a4929 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'GraphViz' +version = '2.18' + +homepage = 'https://metacpan.org/pod/GraphViz' +description = """This module provides a Perl interface to the amazing Graphviz, +an open source graph visualization tool from AT&T.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'] +sources = [SOURCE_TGZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("Graphviz", "2.38.0"), +] + + +options = {'modulename': 'GraphViz'} + +moduleclass = 'vis' -- GitLab From 5ec08a68cbf58b8727cc084c1089a72832f62e8c Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 15:46:24 +0200 Subject: [PATCH 624/992] fixed typo --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index f364f9fafd..cc5cb2cc40 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -1,5 +1,4 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -pts # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -- GitLab From 7f8021baaefe768dfe0dd0cd0f91c64547b21a41 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 12 Aug 2014 10:42:48 +0200 Subject: [PATCH 625/992] Don't run the Bloom tests for Jellyfish, they can randomly fail --- .../easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb index 595bb566df..e874c05030 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -runtest = "check" +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" sanity_check_paths = { 'files': ['bin/jellyfish'], -- GitLab From 4b4938bf43a2cd2d95964ba82d29e7c449352f6b Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Aug 2014 17:35:04 +0200 Subject: [PATCH 626/992] added sailfish, uses c++11, so no full intel support yet --- .../g/g2log/g2log-1.0-foss-2014b.eb | 27 +++++++++++++++ .../Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb | 34 +++++++++++++++++++ .../s/Sailfish/Sailfish-0.6.3-foss-2014b.eb | 30 ++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb new file mode 100644 index 0000000000..3ea56b7193 --- /dev/null +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb @@ -0,0 +1,27 @@ +name = 'g2log' +version = '1.0' +easyblock = 'CMakeMake' + +homepage = 'https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11' +description = """g2log, efficient asynchronous logger using C++11""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://bitbucket.org/KjellKod/g2log/get/'] +sources = ['version-%(version)s.tar.gz'] + +preconfigopts = 'unzip ../3rdParty/gtest/gtest-1.6.0__stripped.zip -d ../3rdParty/gtest/ &&' +preinstallopts = 'mkdir %(installdir)s/lib && cp lib*.a %(installdir)s/lib ||' + +builddependencies = [ + ('CMake', '3.0.0'), +] + +start_dir = 'g2log' +parallel = 1 +moduleclass = 'devel' + +sanity_check_paths = { + 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], + 'dirs': [], +} diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..b8fe958616 --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,34 @@ +name = 'Sailfish' +version = '0.6.3' +easyblock = 'CMakeMake' + +homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' +description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of + isoform abundances directly from a set of reference sequences and RNA-seq reads. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) + +builddependencies = [ + ('CMake', '3.0.0'), +] + +dependencies = [ + ('Boost', '1.55.0', versionsuffix), + ('tbb', '4.0.5.339', '', True), + ('Jellyfish', '2.1.3'), + ('g2log', '1.0'), +] + +preconfigopts = "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTTBB/tbb/include &&" +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" + +parallel = 1 +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb new file mode 100644 index 0000000000..25da9fbb78 --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb @@ -0,0 +1,30 @@ +name = 'Sailfish' +version = '0.6.3' +easyblock = 'CMakeMake' + +homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' +description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of + isoform abundances directly from a set of reference sequences and RNA-seq reads. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) + +builddependencies = [ + ('binutils', '2.24'), + ('CMake', '3.0.0'), +] + +dependencies = [ + ('Boost', '1.55.0', versionsuffix), + ('tbb', '4.0.5.339', '', True), +] + +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" + +moduleclass = 'bio' -- GitLab From 3bae85691d97cd62241c3e09d8071c4146d6bb70 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 26 Aug 2014 15:37:04 +0200 Subject: [PATCH 627/992] added missing dependencies --- .../Boost-1.55.0-foss-2014b-Python-2.7.8.eb | 26 +++++++++++++++++++ .../c/CMake/CMake-2.8.12-foss-2014b.eb | 20 ++++++++++++++ .../j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb | 26 +++++++++++++++++++ 3 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..8d26308267 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,26 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb new file mode 100644 index 0000000000..9aa6ac6517 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb new file mode 100644 index 0000000000..1adc72b8e1 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'Jellyfish' +version = '2.1.3' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" +toolchain = {'name': 'foss', 'version': '2014b'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) + +source_urls = ['ftp://ftp.genome.umd.edu/pub/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 9d5284b392acf12a14e987cc4d8caa6120b2f6e5 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 23 Jan 2015 13:28:07 +0100 Subject: [PATCH 628/992] removed unwanted easyconfig --- .../s/Sailfish/Sailfish-0.6.3-foss-2014b.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb deleted file mode 100644 index 25da9fbb78..0000000000 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b.eb +++ /dev/null @@ -1,30 +0,0 @@ -name = 'Sailfish' -version = '0.6.3' -easyblock = 'CMakeMake' - -homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' -description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of - isoform abundances directly from a set of reference sequences and RNA-seq reads. """ - -toolchain = {'name': 'foss', 'version': '2014b'} - -source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] -sources = ['v%(version)s.tar.gz'] - -python = 'Python' -pyver = '2.7.8' -versionsuffix = '-%s-%s' % (python, pyver) - -builddependencies = [ - ('binutils', '2.24'), - ('CMake', '3.0.0'), -] - -dependencies = [ - ('Boost', '1.55.0', versionsuffix), - ('tbb', '4.0.5.339', '', True), -] - -configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" - -moduleclass = 'bio' -- GitLab From 64eeafd8c47ba44fdb4cec5fa114242187563193 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 23 Jan 2015 13:29:41 +0100 Subject: [PATCH 629/992] fixed remarks --- easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb | 3 ++- .../easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb index 3ea56b7193..342cbc03cb 100644 --- a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb @@ -19,9 +19,10 @@ builddependencies = [ start_dir = 'g2log' parallel = 1 -moduleclass = 'devel' sanity_check_paths = { 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], 'dirs': [], } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb index 1adc72b8e1..10823b3f36 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb @@ -8,7 +8,8 @@ version = '2.1.3' homepage = 'http://www.genome.umd.edu/jellyfish.html' description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" -toolchain = {'name': 'foss', 'version': '2014b'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) + +toolchain = {'name': 'foss', 'version': '2014b'} source_urls = ['ftp://ftp.genome.umd.edu/pub/jellyfish/'] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 4066e7c7762d37c1308a540b62d8a3fb9242a1ea Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 23 Jan 2015 14:56:01 +0100 Subject: [PATCH 630/992] added ConfigureMake where needed --- easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb | 2 ++ easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb | 1 + 2 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb index 9aa6ac6517..08b9903802 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'CMake' version = '2.8.12' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb index 10823b3f36..bd77b8e773 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb @@ -2,6 +2,7 @@ # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' name = 'Jellyfish' version = '2.1.3' -- GitLab From 34cce2fcad0621644e950ac0c88815d14baf1293 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 12:52:55 +0200 Subject: [PATCH 631/992] added CMake 3.0.0-foss-2014b --- .../c/CMake/CMake-3.0.0-foss-2014b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb new file mode 100644 index 0000000000..afa437e164 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '3.0.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From fe7b8fd78399f80a849e1bdc0fcb3a97672369fe Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 13:19:42 +0200 Subject: [PATCH 632/992] Explicitly add easyblock='ConfigureMake' --- easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb index afa437e164..872f8b4d7d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'CMake' version = '3.0.0' -- GitLab From 7ac3150de254be2566bf5ca87bab84e3eebb0063 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:48:36 +0200 Subject: [PATCH 633/992] style fixes in boost easyconfig --- easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index fa03c1c2ae..52215bc3eb 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -14,9 +14,9 @@ dependencies = [('bzip2', '1.0.6')] osdependencies = [('zlib-devel','zlib1g-dev')] +configopts = '--without-libraries=python' + # also build boost_mpi boost_mpi = True -configopts = '--without-libraries=python' - moduleclass = 'devel' -- GitLab From be89f2ec2da4ba5a4255869e8732cfd60707b5f0 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:49:46 +0200 Subject: [PATCH 634/992] use template %(version)s for patch name --- easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb index 2a4b09be4d..d99d70b100 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb @@ -17,7 +17,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] -patches = ['tophat-2.0.13-zlib.patch'] +patches = ['tophat-%(version)s-zlib.patch'] dependencies = [ ('Boost', '1.55.0'), -- GitLab From d7d3960d550a8bd345369795efcd6d9cf6db7ef0 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:51:24 +0200 Subject: [PATCH 635/992] added zlib as eb dependency instead of system dep --- easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb index 52215bc3eb..644fd26b38 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -10,9 +10,9 @@ toolchainopts = {'pic': True, 'usempi': True} sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] source_urls = [SOURCEFORGE_SOURCE] -dependencies = [('bzip2', '1.0.6')] - -osdependencies = [('zlib-devel','zlib1g-dev')] +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8')] configopts = '--without-libraries=python' -- GitLab From e39d1aa90b59708d7ef5be81b46695b6d77262d0 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 3 Jun 2015 09:52:18 -0400 Subject: [PATCH 636/992] moved deps up under source_urls --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 12 ++++++------ easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index ceec29fe23..6a03e95dba 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -25,12 +25,6 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] -preconfigopts = 'make configure && ' - -# Work around git build system bug. If LIBS contains -lpthread, then configure -# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" - dependencies = [ ('cURL', '7.40.0'), ('expat', '2.1.0'), @@ -38,6 +32,12 @@ dependencies = [ ('Perl', '5.20.1', '-bare'), ] +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" + sanity_check_paths = { 'files': ['bin/git'], 'dirs': [], diff --git a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb index d03af57112..ec7ac4488b 100644 --- a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb @@ -25,12 +25,6 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] -preconfigopts = 'make configure && ' - -# Work around git build system bug. If LIBS contains -lpthread, then configure -# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" - dependencies = [ ('cURL', '7.40.0'), ('expat', '2.1.0'), @@ -38,6 +32,12 @@ dependencies = [ ('Perl', '5.20.1', '-bare'), ] +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + sanity_check_paths = { 'files': ['bin/git'], 'dirs': [], -- GitLab From 2d6731ed2480805eb6a25d63835d79472bd830dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 15:53:10 +0200 Subject: [PATCH 637/992] update blasr easyconfig & fix style issues --- .../b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb | 43 --------------- .../blasr-smrtanalysis-2.1-goolf-1.4.10.eb | 52 +++++++++++++++++++ ...> blasr-smrtanalysis-2.1_non-static.patch} | 0 3 files changed, 52 insertions(+), 43 deletions(-) delete mode 100644 easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb rename easybuild/easyconfigs/b/blasr/{non-static.patch => blasr-smrtanalysis-2.1_non-static.patch} (100%) diff --git a/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb deleted file mode 100644 index 5663de6022..0000000000 --- a/easybuild/easyconfigs/b/blasr/blasr-git-smrt2.1-goolf-1.4.10.eb +++ /dev/null @@ -1,43 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for BLASR: -# ---------------------------------------------------------------------------- -# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Petar Forai -# ---------------------------------------------------------------------------- - -name = 'blasr' -version = 'smrtanalysis-2.1' - -easyblock = "MakeCp" - -homepage = 'https://github.com/PacificBiosciences/blasr' -description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" - - -toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} - -#like https://github.com/PacificBiosciences/blasr/archive/smrtanalysis-2.1.tar.gz for tag smnrtanalysis -sources = ['%(version)s.tar.gz'] -source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] - - -patches = ['non-static.patch'] - -files_to_copy = [(['alignment/bin/wordCounter', 'alignment/bin/printReadWordCount', 'alignment/bin/blasr', 'alignment/bin/sdpMatcher', 'alignment/bin/swMatcher', 'alignment/bin/kbandMatcher', 'alignment/bin/sawriter', 'alignment/bin/saquery', 'alignment/bin/samodify', 'alignment/bin/printTupleCountTable', 'alignment/bin/malign', 'alignment/bin/cmpPrintTupleCountTable', 'alignment/bin/removeAdapters', 'alignment/bin/tabulateAlignment', 'alignment/bin/samatcher', 'alignment/bin/sals', 'alignment/bin/saprinter', 'alignment/bin/buildQualityValueProfile', 'alignment/bin/extendAlign', 'alignment/bin/guidedalign', 'alignment/bin/pbmask'],'bin')] - - -sanity_check_paths = { - 'files': ['bin/wordCounter', 'bin/printReadWordCount', 'bin/blasr', 'bin/sdpMatcher', 'bin/swMatcher', 'bin/kbandMatcher', 'bin/sawriter', 'bin/saquery', 'bin/samodify', 'bin/printTupleCountTable', 'bin/malign', 'bin/cmpPrintTupleCountTable', 'bin/removeAdapters', 'bin/tabulateAlignment', 'bin/samatcher', 'bin/sals', 'bin/saprinter', 'bin/buildQualityValueProfile', 'bin/extendAlign', 'bin/guidedalign', 'bin/pbmask'], - 'dirs': [], -} - -makeopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' - -dependencies = [ - ('HDF5', '1.8.9'), -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..0db39afce4 --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -0,0 +1,52 @@ +# With <3 for EasyBuild +# +# EasyConfig for BLASR: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = 'MakeCp' + +name = 'blasr' +version = 'smrtanalysis-2.1' + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" + + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] + +patches = ['blasr-%(version)s_non-static.patch'] + +dependencies = [ + ('HDF5', '1.8.9'), +] + +buildopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' + +files_to_copy = [(['alignment/bin/wordCounter', 'alignment/bin/printReadWordCount', 'alignment/bin/blasr', + 'alignment/bin/sdpMatcher', 'alignment/bin/swMatcher', 'alignment/bin/kbandMatcher', + 'alignment/bin/sawriter', 'alignment/bin/saquery', 'alignment/bin/samodify', + 'alignment/bin/printTupleCountTable', 'alignment/bin/malign', + 'alignment/bin/cmpPrintTupleCountTable', 'alignment/bin/removeAdapters', + 'alignment/bin/tabulateAlignment', 'alignment/bin/samatcher', 'alignment/bin/sals', + 'alignment/bin/saprinter', 'alignment/bin/buildQualityValueProfile', 'alignment/bin/extendAlign', + 'alignment/bin/guidedalign', 'alignment/bin/pbmask'],'bin')] + + +sanity_check_paths = { + 'files': ['bin/wordCounter', 'bin/printReadWordCount', 'bin/blasr', 'bin/sdpMatcher', 'bin/swMatcher', + 'bin/kbandMatcher', 'bin/sawriter', 'bin/saquery', 'bin/samodify', 'bin/printTupleCountTable', + 'bin/malign', 'bin/cmpPrintTupleCountTable', 'bin/removeAdapters', 'bin/tabulateAlignment', + 'bin/samatcher', 'bin/sals', 'bin/saprinter', 'bin/buildQualityValueProfile', 'bin/extendAlign', + 'bin/guidedalign', 'bin/pbmask'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr/non-static.patch b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch similarity index 100% rename from easybuild/easyconfigs/b/blasr/non-static.patch rename to easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch -- GitLab From 623b9a8744d9f9809a3f49c8b86354921bb6dd4a Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 15:56:59 +0200 Subject: [PATCH 638/992] get rid of shared_lib_ext --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index c793f86806..a53d8baacf 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -28,7 +28,7 @@ osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], -- GitLab From 7c76bcac1439ec43ce6d2a4a6e65226c73651c6a Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 15:58:17 +0200 Subject: [PATCH 639/992] readded missing zlib-goolf-1.7.20 easyconfig --- .../z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 977 ++++++++++++++++++ 1 file changed, 977 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb new file mode 100644 index 0000000000..1b7ded7c48 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -0,0 +1,977 @@ + + + + + + + + + + + + easybuild-easyconfigs/zlib-1.2.8-goolf-1.7.20.eb at develop · hpcugent/easybuild-easyconfigs · GitHub + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
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easyblock = 'ConfigureMake'
+
name = 'zlib'
version = '1.2.8'
+
homepage = 'http://www.zlib.net/'
description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is,
not covered by any patents -- lossless data-compression library for use on virtually any
computer hardware and operating system."""
+
toolchain = {'name': 'goolf', 'version': '1.7.20'}
toolchainopts = {'optarch': True, 'pic': True}
+
source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')]
sources = [SOURCELOWER_TAR_GZ]
+
sanity_check_paths = {
'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'],
'dirs': [],
}
+
moduleclass = 'lib'
+ +
+ +
+ +Jump to Line + + +
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+ + + Something went wrong with that request. Please try again. +
+ + + + + + + + + -- GitLab From 5147003a015563b7a0cb65936a8641fe46aa4c88 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 15:58:27 +0200 Subject: [PATCH 640/992] properly fixed .eb name now --- .../t/tecplot360ex/tecplot360ex-linux64.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb new file mode 100644 index 0000000000..08531bb3f3 --- /dev/null +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'tecplot360ex' +version = 'linux64' + +homepage = 'http://www.tecplot.com/' +description = """ + Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, + and communicate your results with professional images and animations. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://www.tecplot.com/my/product-releases/ +installername = '%(name)s_%(version)s.sh' +sources = [installername] + +sanity_check_paths = { + 'files': ['bin/tec360'], + 'dirs': [] +} +install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) + +moduleclass = 'vis' -- GitLab From 2867e79d2362281a15c99490bff3cc4c68fd103d Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 16:03:45 +0200 Subject: [PATCH 641/992] added right zlib easyconfig --- .../z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 987 +----------------- 1 file changed, 16 insertions(+), 971 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb index 1b7ded7c48..2e006a7aca 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -1,977 +1,22 @@ +easyblock = 'ConfigureMake' +name = 'zlib' +version = '1.2.8' +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" - - - - - - - - - easybuild-easyconfigs/zlib-1.2.8-goolf-1.7.20.eb at develop · hpcugent/easybuild-easyconfigs · GitHub - - - - - - - +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} - - - - - - - - +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +sources = [SOURCELOWER_TAR_GZ] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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easyblock = 'ConfigureMake'
-
name = 'zlib'
version = '1.2.8'
-
homepage = 'http://www.zlib.net/'
description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is,
not covered by any patents -- lossless data-compression library for use on virtually any
computer hardware and operating system."""
-
toolchain = {'name': 'goolf', 'version': '1.7.20'}
toolchainopts = {'optarch': True, 'pic': True}
-
source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')]
sources = [SOURCELOWER_TAR_GZ]
-
sanity_check_paths = {
'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'],
'dirs': [],
}
-
moduleclass = 'lib'
- -
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- - - - - - - - +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} +moduleclass = 'lib' -- GitLab From c6f55c370d466780d4cc7055e3384478b32f7f15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 16:03:52 +0200 Subject: [PATCH 642/992] fix long line --- .../b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb index 0db39afce4..44a2388e5e 100644 --- a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -13,7 +13,9 @@ name = 'blasr' version = 'smrtanalysis-2.1' homepage = 'https://github.com/PacificBiosciences/blasr' -description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" +description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the + highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's + extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 5e8e28a8dd7a03eedc020708f7384c196422e25f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 16:16:33 +0200 Subject: [PATCH 643/992] removed old file --- .../t/tecplot360ex/tecplot-360ex.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb deleted file mode 100644 index 08531bb3f3..0000000000 --- a/easybuild/easyconfigs/t/tecplot360ex/tecplot-360ex.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'Binary' - -name = 'tecplot360ex' -version = 'linux64' - -homepage = 'http://www.tecplot.com/' -description = """ - Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, - and communicate your results with professional images and animations. -""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# fi. http://www.tecplot.com/my/product-releases/ -installername = '%(name)s_%(version)s.sh' -sources = [installername] - -sanity_check_paths = { - 'files': ['bin/tec360'], - 'dirs': [] -} -install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) - -moduleclass = 'vis' -- GitLab From e7194f07e4d1c4257263134c7ed677caaa36f807 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 16:44:23 +0200 Subject: [PATCH 644/992] fix style remarks --- .../blasr-smrtanalysis-2.1-goolf-1.4.10.eb | 26 +++++++------------ 1 file changed, 9 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb index 44a2388e5e..31e32665e9 100644 --- a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -17,7 +17,6 @@ description = """BLASR (Basic Local Alignment with Successive Refinement) rapidl highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" - toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} @@ -26,28 +25,21 @@ source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] patches = ['blasr-%(version)s_non-static.patch'] -dependencies = [ - ('HDF5', '1.8.9'), -] +dependencies = [('HDF5', '1.8.9')] buildopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' -files_to_copy = [(['alignment/bin/wordCounter', 'alignment/bin/printReadWordCount', 'alignment/bin/blasr', - 'alignment/bin/sdpMatcher', 'alignment/bin/swMatcher', 'alignment/bin/kbandMatcher', - 'alignment/bin/sawriter', 'alignment/bin/saquery', 'alignment/bin/samodify', - 'alignment/bin/printTupleCountTable', 'alignment/bin/malign', - 'alignment/bin/cmpPrintTupleCountTable', 'alignment/bin/removeAdapters', - 'alignment/bin/tabulateAlignment', 'alignment/bin/samatcher', 'alignment/bin/sals', - 'alignment/bin/saprinter', 'alignment/bin/buildQualityValueProfile', 'alignment/bin/extendAlign', - 'alignment/bin/guidedalign', 'alignment/bin/pbmask'],'bin')] +binaries = [ + 'wordCounter', 'printReadWordCount', 'blasr', 'sdpMatcher', 'swMatcher', 'kbandMatcher', 'sawriter', + 'saquery', 'samodify', 'printTupleCountTable', 'malign', 'cmpPrintTupleCountTable', 'removeAdapters', + 'tabulateAlignment', 'samatcher', 'sals', 'saprinter', 'buildQualityValueProfile', 'extendAlign', + 'guidedalign', 'pbmask', +] +files_to_copy = [(['alignment/bin/%s' x for x in binaries], 'bin')] sanity_check_paths = { - 'files': ['bin/wordCounter', 'bin/printReadWordCount', 'bin/blasr', 'bin/sdpMatcher', 'bin/swMatcher', - 'bin/kbandMatcher', 'bin/sawriter', 'bin/saquery', 'bin/samodify', 'bin/printTupleCountTable', - 'bin/malign', 'bin/cmpPrintTupleCountTable', 'bin/removeAdapters', 'bin/tabulateAlignment', - 'bin/samatcher', 'bin/sals', 'bin/saprinter', 'bin/buildQualityValueProfile', 'bin/extendAlign', - 'bin/guidedalign', 'bin/pbmask'], + 'files': ['bin/%s' % x for x in binaries], 'dirs': [], } -- GitLab From 8300b3c48cb90f7c4ed4a56ae1cfab0d879aa41d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 16:52:20 +0200 Subject: [PATCH 645/992] fix typo --- .../easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb index 31e32665e9..d339980b4f 100644 --- a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -36,7 +36,7 @@ binaries = [ 'guidedalign', 'pbmask', ] -files_to_copy = [(['alignment/bin/%s' x for x in binaries], 'bin')] +files_to_copy = [(['alignment/bin/%s' % x for x in binaries], 'bin')] sanity_check_paths = { 'files': ['bin/%s' % x for x in binaries], -- GitLab From 4231891afb0d0cfc6ee47eb7c2702bf3b14013f8 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 16:54:31 +0200 Subject: [PATCH 646/992] changed url --- easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb index 08531bb3f3..40607b6960 100644 --- a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb @@ -3,7 +3,7 @@ easyblock = 'Binary' name = 'tecplot360ex' version = 'linux64' -homepage = 'http://www.tecplot.com/' +homepage = 'http://www.tecplot.com/products/tecplot-360/' description = """ Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, and communicate your results with professional images and animations. -- GitLab From 8b83f0ef72d0a2f1bfb77386455d25d56706b3ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 16:56:11 +0200 Subject: [PATCH 647/992] style fixes in PLUMED easyconfig --- .../PLUMED-2.0.4-ictce-7.1.2.eb} | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/p/{plumed/plumed-2.0.4-ictce-7.1.2.eb => PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb} (50%) diff --git a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb similarity index 50% rename from easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb rename to easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb index 3eda065ef1..aaa2734422 100644 --- a/easybuild/easyconfigs/p/plumed/plumed-2.0.4-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb @@ -1,25 +1,22 @@ -# This is a quickly made easyconfig, using some dirty tricks... -# Warning: Here be dragons # by Ward Poelmans easyblock = 'ConfigureMake' -name = 'plumed' +name = 'PLUMED' version = '2.0.4' homepage = 'http://www.plumed-code.org' description = """PLUMED is an open source library for free energy calculations in molecular systems which -works together with some of the most popular molecular dynamics engines. Free energy calculations can be -performed as a function of many order parameters with a particular focus on biological problems, using -state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. -The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. """ toolchain = {'name': 'ictce', 'version': '7.1.2'} -# Download from http://www.plumed-code.org/get-it, google drive doesn't allow for clean download url source_urls = ['https://github.com/plumed/plumed2/archive/'] -sources = ['v2.0.4.tar.gz'] +sources = ['v%(version)s.tar.gz'] patches = ['configure-%(version)s.patch'] @@ -31,7 +28,6 @@ sanity_check_paths = { 'dirs': ['lib/plumed'] } -# should probably happen in a easyblock. This vars needs to be set modextrapaths = {'PLUMED_KERNEL': 'lib/libplumedKernel.so'} moduleclass = 'chem' -- GitLab From ba3328abf9f4af33dc63bc71c8a472e4c3220a0b Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 17:00:18 +0200 Subject: [PATCH 648/992] fixed remarks --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index cc5cb2cc40..8821d58210 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -11,6 +11,7 @@ version = '0.2.6' homepage = 'http://samtools.sourceforge.net' description = """ Generic indexer for TAB-delimited genome position files """ + toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] -- GitLab From a133fd1d6d12dc26202cf39ce7b8465b6f1ee3ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 17:10:16 +0200 Subject: [PATCH 649/992] move/rename patch for PLUMED --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb | 2 +- .../PLUMED-2.0.4_eb-env-vars.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/{plumed/configure-2.0.4.patch => PLUMED/PLUMED-2.0.4_eb-env-vars.patch} (100%) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb index aaa2734422..b6955fcdcc 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} source_urls = ['https://github.com/plumed/plumed2/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['configure-%(version)s.patch'] +patches = ['PLUMED-%(version)s_eb-env-vars.patch'] preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " diff --git a/easybuild/easyconfigs/p/plumed/configure-2.0.4.patch b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch similarity index 100% rename from easybuild/easyconfigs/p/plumed/configure-2.0.4.patch rename to easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch -- GitLab From 44d2e4e1f678d3006e1ba5cc0aed04b9893094d6 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 18:16:05 +0200 Subject: [PATCH 650/992] fixed patch file --- .../easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch index 278b2edf59..6021cbe107 100644 --- a/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch +++ b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch @@ -1,12 +1,12 @@ diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile ---- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 -+++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-03-14 23:21:04.221640935 +0100 +--- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 ++++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-06-03 18:10:39.588554000 +0200 @@ -12,7 +12,7 @@ - PROG= samtools_0.1.18 - INCLUDES= -I. - SUBDIRS= . bcftools + PROG= samtools_0.1.18 + INCLUDES= -I. + SUBDIRS= . bcftools -LIBPATH= +LIBPATH= -L$(EBROOTZLIB)/lib - LIBCURSES= -lcurses - + LIBCURSES= -lcurses + .SUFFIXES:.c .o -- GitLab From 2bb7142c64e9986632e75caff64e49854dd3da1d Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 18:26:52 +0200 Subject: [PATCH 651/992] fixed remarks --- ...apps.eb => ECore-1.5.2-ictce-5.5.0-clusterapps.eb} | 11 ++++++----- .../{ECore-1.5.2.eb => ECore-1.5.2-ictce-5.5.0.eb} | 7 ++++--- 2 files changed, 10 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/e/ECore/{ECore-1.5.2-clusterapps.eb => ECore-1.5.2-ictce-5.5.0-clusterapps.eb} (71%) rename easybuild/easyconfigs/e/ECore/{ECore-1.5.2.eb => ECore-1.5.2-ictce-5.5.0.eb} (76%) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb similarity index 71% rename from easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb rename to easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb index 6bfb37241d..4975ea635d 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb @@ -5,20 +5,21 @@ version = '1.5.2' versionsuffix = '-clusterapps' homepage = 'http://www.numericalrocks.com/index.php?option=com_content&task=blogcategory&id=25&Itemid=25' -description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. sedimentation, compaction and diagenesis.""" +description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. + sedimentation, compaction and diagenesis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} -sources = ['%s-%s%s.tgz' % (name.lower(), version, versionsuffix)] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz')] patches = ['ecore-license-var.patch'] # needs to be 1.4.x, because it's linked with the libmpi_cxx.so.0 -dependencies = [('OpenMPI', '1.4.5', '-ictce-5.5.0')] +dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { 'files': ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['absperm', 'FormationFactor', 'nmr', - 'orterun', 'packer', 'randomwalkffmpi', + 'orterun', 'packer', 'randomwalkffmpi', 'unpacker']] + \ ['absperm.sh', 'formationfactor.sh', 'nmr.sh', 'rw_formationfactor.sh'], 'dirs': [], diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb similarity index 76% rename from easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb rename to easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb index 5e6f6b0b1c..7c028041b8 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb @@ -4,15 +4,16 @@ name = 'ECore' version = '1.5.2' homepage = 'http://www.numericalrocks.com/index.php?option=com_content&task=blogcategory&id=25&Itemid=25' -description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. sedimentation, compaction and diagenesis.""" +description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. + sedimentation, compaction and diagenesis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -dependencies = [('OpenMPI', '1.4.5', '-ictce-5.5.0')] +dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ -- GitLab From fb559c91cb226728656a55ae6fe057cd7340f69d Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 18:37:22 +0200 Subject: [PATCH 652/992] fixed typo --- .../easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb index 4975ea635d..ca072da66b 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb @@ -10,7 +10,7 @@ description = """The e-Core technology simulates the natural processes of sedime toolchain = {'name': 'ictce', 'version': '5.5.0'} -sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz')] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] patches = ['ecore-license-var.patch'] -- GitLab From 7bf7620290126a28b9f8fe49e169f5553339a52b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 18:44:26 +0200 Subject: [PATCH 653/992] include missing libxml2 dep in GLib easyconfigs --- .../g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb | 1 + .../g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb | 1 + .../GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb | 1 + .../g/GLib/GLib-2.34.3-goolf-1.4.10.eb | 1 + .../g/GLib/GLib-2.34.3-goolf-1.5.14.eb | 1 + .../g/GLib/GLib-2.34.3-ictce-4.0.6.eb | 1 + .../g/GLib/GLib-2.34.3-ictce-4.1.13.eb | 1 + .../g/GLib/GLib-2.34.3-ictce-5.2.0.eb | 1 + .../g/GLib/GLib-2.34.3-ictce-5.3.0.eb | 1 + .../g/GLib/GLib-2.40.0-goolf-1.5.14.eb | 1 + .../g/GLib/GLib-2.40.0-intel-2014.06.eb | 1 + .../g/GLib/GLib-2.40.0-intel-2014b.eb | 1 + .../g/GLib/GLib-2.40.0-intel-2015a.eb | 2 ++ .../g/GLib/GLib-2.41.2-intel-2014b.eb | 1 + .../g/GLib/GLib-2.42.1-GCC-4.9.2.eb | 1 + .../g/GLib/GLib-2.42.1-foss-2015a.eb | 2 ++ .../l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb | 23 +++++++++++++++++++ .../l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb | 22 ++++++++++++++++++ .../l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb | 23 +++++++++++++++++++ .../l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb | 23 +++++++++++++++++++ .../z/zlib/zlib-1.2.7-GCC-4.6.3.eb | 22 ++++++++++++++++++ .../z/zlib/zlib-1.2.7-GCC-4.7.2.eb | 22 ++++++++++++++++++ .../z/zlib/zlib-1.2.7-GCC-4.7.3.eb | 22 ++++++++++++++++++ .../z/zlib/zlib-1.2.8-GCC-4.8.3.eb | 22 ++++++++++++++++++ 28 files changed, 285 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb index 0154f92cba..712b89daa3 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.8.1')), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb index b3f747f733..73f392ace7 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.6.3')), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb index 33fdefa087..2dfca0139b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.7.3')), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb index fe8be618bc..0b921d9d01 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.7.2')), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb index 524a65b421..3abdd2956b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1', '', ('GCC', '4.8.2')), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb index 7330ea1391..1aa508846f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.1.13.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.1.13.eb index 66974822a8..81bd44a395 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.1.13.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.2.0.eb index 6e94d0afc6..f5ec30578d 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.2.0.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb index d913bace56..592b0e9587 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb index 70218fe010..ddf2f99faa 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.8.2')), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb index 0b2f10e82d..18e101a94a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb index be10bd30c3..73012be0a1 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb index 6732978735..ba5297e69e 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb @@ -15,6 +15,8 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.9.2')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index cec860f2de..cf844710e9 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -14,6 +14,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb index 8db2b243a8..acba6c86f0 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb @@ -15,6 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb index 167d8fc75b..aa417b69e0 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb @@ -15,6 +15,8 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), + ('libxml2', '2.9.2'), + ('libxml2', '2.9.2', '', ('GCC', '4.9.2')), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb new file mode 100644 index 0000000000..f23eb301d6 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.6.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb new file mode 100644 index 0000000000..c70f20afe3 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.7.2'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb new file mode 100644 index 0000000000..8a43c4c25e --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb new file mode 100644 index 0000000000..c26849960b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.1'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb new file mode 100644 index 0000000000..c19288a2fa --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb new file mode 100644 index 0000000000..232c2e480f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'ictce', 'version': '5.2.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb new file mode 100644 index 0000000000..4fc4a74955 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb new file mode 100644 index 0000000000..9291662776 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb new file mode 100644 index 0000000000..a6b6f7f14b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCC', 'version': '4.6.3'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb new file mode 100644 index 0000000000..f2216d86e1 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCC', 'version': '4.7.2'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb new file mode 100644 index 0000000000..572b633565 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb new file mode 100644 index 0000000000..1a28c0fbf0 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, +not covered by any patents -- lossless data-compression library for use on virtually any +computer hardware and operating system.""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From fba60a93b13e73b907a4b14174e10e260a3846ed Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 3 Jun 2015 19:18:17 +0200 Subject: [PATCH 654/992] fixed remarks --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb index 808db8594a..4ab3c4b882 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -19,6 +19,8 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), (["tabix.1"], "man/man1"), @@ -27,7 +29,6 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index 8821d58210..355e0eb0ad 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -19,6 +19,8 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), (["tabix.1"], "man/man1"), @@ -27,7 +29,6 @@ files_to_copy = [ "NEWS", "ChangeLog" ] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' sanity_check_paths = { 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], -- GitLab From dabb53e8595bb31e25365f5926bd8bfd8cb6b85d Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 19:18:42 +0200 Subject: [PATCH 655/992] fixed small style remarks by @fgeorgatos --- easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb index aaedf45292..486d2e128c 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb @@ -28,8 +28,7 @@ files_to_copy = [(["STAR"], "bin"), "README.txt"] sanity_check_paths = { 'files': ["bin/STAR"], - 'dirs': [""], + 'dirs': [], } moduleclass = 'bio' - -- GitLab From 589703db14101b2cfc569f6bcaf60da1f97e7109 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 19:23:03 +0200 Subject: [PATCH 656/992] style fixes --- .../s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb index 76fe9f0898..a4cefde064 100644 --- a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -35,7 +35,7 @@ options = {'modulename': 'POSIX'} sanity_check_paths = { 'files': ["bin/scanms"], - 'dirs': [""] + 'dirs': [] } # copy all the documentation provided in the tarball to install directory -- GitLab From 024e73ba8320b97706e8b7c4521dd64d27068057 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 20:17:33 +0200 Subject: [PATCH 657/992] bump tophat version --- .../t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb | 36 +++++++++++++++++++ .../t/TopHat/tophat-2.0.14-zlib.patch | 12 +++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb new file mode 100644 index 0000000000..c12d3673ed --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.0.14' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = ['tophat-%(version)s-zlib.patch'] + +dependencies = [ + ('Boost', '1.55.0'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch new file mode 100644 index 0000000000..6021cbe107 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch @@ -0,0 +1,12 @@ +diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile +--- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 ++++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-06-03 18:10:39.588554000 +0200 +@@ -12,7 +12,7 @@ + PROG= samtools_0.1.18 + INCLUDES= -I. + SUBDIRS= . bcftools +-LIBPATH= ++LIBPATH= -L$(EBROOTZLIB)/lib + LIBCURSES= -lcurses + + .SUFFIXES:.c .o -- GitLab From fc4a6d0e7227e2bda414fbcdb1450e336fa7e921 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 20:28:09 +0200 Subject: [PATCH 658/992] removed duplicated patch file --- .../t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb | 2 +- .../easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch | 12 ------------ 2 files changed, 1 insertion(+), 13 deletions(-) delete mode 100644 easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb index c12d3673ed..a2c8c49b14 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb @@ -17,7 +17,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] -patches = ['tophat-%(version)s-zlib.patch'] +patches = ['tophat-2.0.13-zlib.patch'] dependencies = [ ('Boost', '1.55.0'), diff --git a/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch deleted file mode 100644 index 6021cbe107..0000000000 --- a/easybuild/easyconfigs/t/TopHat/tophat-2.0.14-zlib.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile ---- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 -+++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-06-03 18:10:39.588554000 +0200 -@@ -12,7 +12,7 @@ - PROG= samtools_0.1.18 - INCLUDES= -I. - SUBDIRS= . bcftools --LIBPATH= -+LIBPATH= -L$(EBROOTZLIB)/lib - LIBCURSES= -lcurses - - .SUFFIXES:.c .o -- GitLab From 361318413eff3b032094994d011c9b084e434d39 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 20:48:24 +0200 Subject: [PATCH 659/992] removed sanity check hack --- .../s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb index a4cefde064..b40b1b8d7a 100644 --- a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -29,9 +29,8 @@ dependencies = [ (perl, perlver), ] -# workaround so sanity check in the PerlModule easyblock works. -# Just check the existence of a perl core module -options = {'modulename': 'POSIX'} +# override the default sanity check for perl packages which tries to load Perl module +exts_filter = ('scanms -v 2>&1 | grep version', "") sanity_check_paths = { 'files': ["bin/scanms"], -- GitLab From 83d0b63e4b843b26d9ec83e5a0ee23384fa17c12 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:00:25 +0200 Subject: [PATCH 660/992] switch from premakeopts to prebuildopts --- easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb index 486d2e128c..c428723fec 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb @@ -20,7 +20,7 @@ sources = ['%(name)s_%(version)s.tgz'] patches = ['STAR_missing_includes.patch'] # a binary is provided with the source files. We delete it -premakeopts = 'rm STAR && ' +prebuildopts = 'rm STAR && ' parallel = 1 -- GitLab From f4979b40b64b15a803076bacd4b615022c889e52 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:06:15 +0200 Subject: [PATCH 661/992] style fixes in files_to_copy --- .../p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index f573781fab..1ac74ecb09 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -24,9 +24,15 @@ dependencies = [('SAMtools', '0.1.19')] cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] -files_to_copy = [(['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), - "demo", "gmt", "gmt-web", "test", "README.md", "RELEASE" - ] +files_to_copy = [ + (['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), + "demo", + "gmt", + "gmt-web", + "test", + "README.md", + "RELEASE" +] postinstallcmds = ["sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bam2pindel.pl"] -- GitLab From 3e2900d865cbf1071920a0a5d686fcdc39854b55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 21:06:46 +0200 Subject: [PATCH 662/992] add missing easyblock spec --- easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb index 742fe0d215..d4e5cc4292 100644 --- a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'LAMARC' version = '2.1.9' versionsuffix = '-headless' -- GitLab From 0a7faf654af73591e753d7e399d87e442efa82cd Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:11:19 +0200 Subject: [PATCH 663/992] added missing zlib dependency --- .../easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 1ac74ecb09..3f76c20eb4 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -20,7 +20,10 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/genome/pindel/archive/'] sources = ['v%(version)s.tar.gz'] -dependencies = [('SAMtools', '0.1.19')] +dependencies = [ + ('SAMtools', '0.1.19'), + ('zlib', '1.2.8') +] cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] -- GitLab From 508c3e22b75d2aea284e3b97aa30ebbec3ab2f84 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:17:55 +0200 Subject: [PATCH 664/992] removed post install cmds, added patch --- .../easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch | 9 +++++++++ 2 files changed, 11 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 3f76c20eb4..41822a6052 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -20,6 +20,8 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/genome/pindel/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['pindel-perl-path.patch'] + dependencies = [ ('SAMtools', '0.1.19'), ('zlib', '1.2.8') @@ -37,8 +39,6 @@ files_to_copy = [ "RELEASE" ] -postinstallcmds = ["sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bam2pindel.pl"] - sanity_check_paths = { 'files': ['bin/pindel', 'bin/sam2pindel', 'bin/pindel2vcf', 'bin/bam2pindel.pl'], 'dirs': [], diff --git a/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch b/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch new file mode 100644 index 0000000000..db0214c680 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch @@ -0,0 +1,9 @@ +diff -ru pindel-0.2.5a7.orig/bam2pindel.pl pindel-0.2.5a7/bam2pindel.pl +--- pindel-0.2.5a7.orig/bam2pindel.pl 2014-09-16 20:53:13.000000000 +0200 ++++ pindel-0.2.5a7/bam2pindel.pl 2015-06-03 21:12:57.775900885 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/env perl + + ######################################################################################################## + # # -- GitLab From 97eaf188766668743df86babdb1efdd452451f39 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:21:03 +0200 Subject: [PATCH 665/992] switched to prebuildopts --- easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb index 43d9e4ed11..92c332b06d 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -28,7 +28,7 @@ sources = ['idba-%(version)s.tar.gz'] premakeopts = './configure && ' # we delete every .o file which is left in bin folder -makeopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' +buildopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' files_to_copy = ["bin", "script", "README", "ChangeLog", "NEWS"] @@ -39,4 +39,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From 68bdbcd2d19a172064d419bb816ca938bda550a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 21:21:50 +0200 Subject: [PATCH 666/992] fix typo --- .../b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb index e24751cd72..5954f54393 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb @@ -10,7 +10,7 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] -sources = ['bioperl-release-%s.tar.gz' % version.replace('.', '-')] +sources = ['release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.18.2' -- GitLab From ebc370953e34d38dd9020e14ec2152877671df27 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:24:26 +0200 Subject: [PATCH 667/992] switched to prebuildopts --- easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb index 92c332b06d..0ee4a4f740 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -25,7 +25,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://hku-idba.googlecode.com/files/'] sources = ['idba-%(version)s.tar.gz'] -premakeopts = './configure && ' +prebuildopts = './configure && ' # we delete every .o file which is left in bin folder buildopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' -- GitLab From 7aa4fbb40ec156297b18592fafa388ea5c809823 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:27:00 +0200 Subject: [PATCH 668/992] added missing easyblock line --- easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb index e63d0852ef..665f1371cb 100644 --- a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = "Check" version = "0.9.12" -- GitLab From 8bab0c90523ae32e3688a9e107425281f41b75da Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:28:47 +0200 Subject: [PATCH 669/992] fixed indentation --- .../s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb index b40b1b8d7a..88fe827b03 100644 --- a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -33,8 +33,8 @@ dependencies = [ exts_filter = ('scanms -v 2>&1 | grep version', "") sanity_check_paths = { - 'files': ["bin/scanms"], - 'dirs': [] + 'files': ["bin/scanms"], + 'dirs': [] } # copy all the documentation provided in the tarball to install directory -- GitLab From 26d6ec222c34367c74c82a1c7cb28ea400eb67b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 21:29:25 +0200 Subject: [PATCH 670/992] fix LAMARC filename --- ...-2.1.9-ictce-5.5.0.eb => LAMARC-2.1.9-ictce-5.5.0-headless.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/LAMARC/{LAMARC-2.1.9-ictce-5.5.0.eb => LAMARC-2.1.9-ictce-5.5.0-headless.eb} (100%) diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb similarity index 100% rename from easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0.eb rename to easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb -- GitLab From 5949aa6043031d72e35405904d82e2dac095b680 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:32:13 +0200 Subject: [PATCH 671/992] renamed as @boegel suggested --- ...k_Vina-1.1.2-linux_x86.eb => AutoDock_Vina-1.1.2_linux_x86.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/AutoDock_Vina/{AutoDock_Vina-1.1.2-linux_x86.eb => AutoDock_Vina-1.1.2_linux_x86.eb} (100%) diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb similarity index 100% rename from easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2-linux_x86.eb rename to easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb -- GitLab From a30448b8157c934c9778570454a7670984cb1be1 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:35:16 +0200 Subject: [PATCH 672/992] switched to zlib-1.2.7 --- easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index 41822a6052..65d0c45c59 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -24,7 +24,7 @@ patches = ['pindel-perl-path.patch'] dependencies = [ ('SAMtools', '0.1.19'), - ('zlib', '1.2.8') + ('zlib', '1.2.7') ] cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] -- GitLab From 73c49e1cc1bff2877cce7dd1b2d6d1ea34915357 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:43:15 +0200 Subject: [PATCH 673/992] added Boost-1.58.0-goolf-1.7.20.eb --- .../b/Boost/Boost-1.58.0-goolf-1.7.20.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..8f65c8b894 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8')] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 91f2b1d488c0725723a731eb56ad51d5744f6a1d Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:43:56 +0200 Subject: [PATCH 674/992] bump to latest boost in tophat easyconfig --- easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb index a2c8c49b14..6743572399 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb @@ -20,7 +20,7 @@ source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] patches = ['tophat-2.0.13-zlib.patch'] dependencies = [ - ('Boost', '1.55.0'), + ('Boost', '1.58.0'), ('zlib', '1.2.8'), ] -- GitLab From 8ae3cf405b4060a3d3d6d492798c6ea30fb755bc Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:48:55 +0200 Subject: [PATCH 675/992] renamed as @boegel suggested --- ...E2-2.3.0-x86_64_dynamic.eb => IMPUTE2-2.3.0_x86_64_dynamic.eb} | 0 ...UTE2-2.3.0-x86_64_static.eb => IMPUTE2-2.3.0_x86_64_static.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/IMPUTE2/{IMPUTE2-2.3.0-x86_64_dynamic.eb => IMPUTE2-2.3.0_x86_64_dynamic.eb} (100%) rename easybuild/easyconfigs/i/IMPUTE2/{IMPUTE2-2.3.0-x86_64_static.eb => IMPUTE2-2.3.0_x86_64_static.eb} (100%) diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb similarity index 100% rename from easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_dynamic.eb rename to easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb similarity index 100% rename from easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0-x86_64_static.eb rename to easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb -- GitLab From 338788f1318b804748052fb9c6ec64ba2b644d7b Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Wed, 3 Jun 2015 21:51:37 +0200 Subject: [PATCH 676/992] moved easyblock line to top --- .../c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb index 815406dfba..f772aaa29c 100644 --- a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb @@ -3,11 +3,11 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'MakeCp' + name = 'CONTRAfold' version = '2.02' -easyblock = 'MakeCp' - homepage = 'http://contra.stanford.edu/contrafold/' description = ''' CONditional TRAining for RNA Secondary Structure Prediction ''' @@ -21,7 +21,7 @@ patches = ['contrafold-gcc47.patch'] start_dir = 'src' files_to_copy = [(['score_prediction', 'contrafold', 'score_directory.pl',\ - 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] sanity_check_paths = { 'files': ['bin/score_prediction', 'bin/contrafold'], -- GitLab From 4ed7c6cea54b2608edda2ed5878ae14922900a24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 08:36:02 +0200 Subject: [PATCH 677/992] fix style issue --- easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb index 8f65c8b894..bee3eb38e4 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb @@ -12,7 +12,8 @@ source_urls = [SOURCEFORGE_SOURCE] dependencies = [ ('bzip2', '1.0.6'), - ('zlib', '1.2.8')] + ('zlib', '1.2.8'), +] configopts = '--without-libraries=python' -- GitLab From ab02f47ebfbff434dc834e7217c01c759bac2911 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 11:08:00 +0200 Subject: [PATCH 678/992] {toolchain} GNU 5.1.0-2.25 --- .../binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 35 +++++++++++++ .../g/GCC/GCC-5.1.0-binutils-2.25.eb | 52 +++++++++++++++++++ easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb | 20 +++++++ .../zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb | 23 ++++++++ 4 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000..fa4ce3cee9 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-%(version)s'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('zlib', '1.2.8'), + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000..b9370c56ff --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,52 @@ +name = "GCC" +version = '5.1.0' + +binutilsver = '2.25' +versionsuffix = '-binutils-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +builddependencies = [('binutils', binutilsver)] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..684b3462cf --- /dev/null +++ b/easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'GNU' +gccver = '5.1.0' +binutilsver = '2.25' +version = '%s-%s' % (gccver, binutilsver) + +homepage = 'http://www.gnu.org/software/' +description = "Compiler-only toolchain with GCC and binutils." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # GCC built on top of (dummy-built) binutils + ('GCC', gccver, '-binutils-%s' % binutilsver), + # binutils built on top of GCC, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCC', '%s-binutils-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000..d10f6ce0ce --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +builddependencies = [('binutils', '2.25', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 132a763aab0d19da7882a8c8f3c8f849f60b00f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 12:39:15 +0200 Subject: [PATCH 679/992] fix toolchain for libxml2 deps in GLib easyconfigs --- .../g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb | 2 +- .../g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb | 2 +- .../GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb | 2 +- .../g/GLib/GLib-2.34.3-goolf-1.4.10.eb | 2 +- .../g/GLib/GLib-2.34.3-goolf-1.5.14.eb | 2 +- .../g/GLib/GLib-2.40.0-goolf-1.5.14.eb | 2 +- .../g/GLib/GLib-2.40.0-intel-2014.06.eb | 2 +- .../g/GLib/GLib-2.40.0-intel-2014b.eb | 2 +- .../g/GLib/GLib-2.40.0-intel-2015a.eb | 1 - .../g/GLib/GLib-2.41.2-intel-2014b.eb | 2 +- .../l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb | 22 ------------------- ...4.6.3.eb => libxml2-2.9.1-gmpolf-1.4.8.eb} | 2 +- ... => libxml2-2.9.1-gompi-1.4.12-no-OFED.eb} | 2 +- ...4.7.2.eb => libxml2-2.9.1-goolf-1.5.14.eb} | 2 +- ...4.8.3.eb => libxml2-2.9.2-goolf-1.5.14.eb} | 2 +- ....8.2.eb => libxml2-2.9.2-intel-2014.06.eb} | 6 ++--- ...-4.8.2.eb => libxml2-2.9.2-intel-2014b.eb} | 2 +- .../z/zlib/zlib-1.2.7-GCC-4.6.3.eb | 22 ------------------- .../z/zlib/zlib-1.2.7-GCC-4.7.2.eb | 22 ------------------- .../z/zlib/zlib-1.2.7-GCC-4.7.3.eb | 22 ------------------- .../z/zlib/zlib-1.2.8-GCC-4.8.3.eb | 22 ------------------- 21 files changed, 17 insertions(+), 128 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.1-GCC-4.6.3.eb => libxml2-2.9.1-gmpolf-1.4.8.eb} (90%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.1-GCC-4.7.3.eb => libxml2-2.9.1-gompi-1.4.12-no-OFED.eb} (89%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.1-GCC-4.7.2.eb => libxml2-2.9.1-goolf-1.5.14.eb} (90%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.2-GCC-4.8.3.eb => libxml2-2.9.2-goolf-1.5.14.eb} (90%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.1-GCC-4.8.2.eb => libxml2-2.9.2-intel-2014.06.eb} (80%) rename easybuild/easyconfigs/l/libxml2/{libxml2-2.9.2-GCC-4.8.2.eb => libxml2-2.9.2-intel-2014b.eb} (90%) delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb index 712b89daa3..d6ca2142ee 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.8.1')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb index 73f392ace7..810a19f768 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.6.3')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb index 2dfca0139b..c01d10d566 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.7.3')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb index 0b921d9d01..767bcb84db 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.7.2')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb index 3abdd2956b..4ce11348bb 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.5.14.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1', '', ('GCC', '4.8.2')), + ('libxml2', '2.9.1'), ] builddependencies = [('Python', '2.7.3')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb index ddf2f99faa..a72a4d209a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.5.14.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.8.2')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb index 18e101a94a..f22199ae2b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb index 73012be0a1..feabab52c2 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014b.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb index ba5297e69e..f5b201076b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2015a.eb @@ -16,7 +16,6 @@ dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), ('libxml2', '2.9.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.9.2')), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb index cf844710e9..207b74b508 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.41.2-intel-2014b.eb @@ -14,7 +14,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.1'), ('gettext', '0.19.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.8.3')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb deleted file mode 100644 index c26849960b..0000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.1.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxml2' -version = '2.9.1' - -homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable -outside of the Gnome platform).""" - -toolchain = {'name': 'GCC', 'version': '4.8.1'} - -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] - -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' - -dependencies = [('zlib', '1.2.7')] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb similarity index 90% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb index f23eb301d6..4f35163694 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb @@ -7,7 +7,7 @@ homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" -toolchain = {'name': 'GCC', 'version': '4.6.3'} +toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb similarity index 89% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index 8a43c4c25e..6e4ab86218 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -7,7 +7,7 @@ homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" -toolchain = {'name': 'GCC', 'version': '4.7.3'} +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb similarity index 90% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb index c70f20afe3..42fd9996e9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb @@ -7,7 +7,7 @@ homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" -toolchain = {'name': 'GCC', 'version': '4.7.2'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb similarity index 90% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb index 9291662776..e2bb547666 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb @@ -8,7 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" -toolchain = {'name': 'GCC', 'version': '4.8.3'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb similarity index 80% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb index c19288a2fa..aae9d0148e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -1,14 +1,14 @@ easyblock = 'ConfigureMake' name = 'libxml2' -version = '2.9.1' +version = '2.9.2' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" -toolchain = {'name': 'GCC', 'version': '4.8.2'} +toolchain = {'name': 'intel', 'version': '2014.06'} source_urls = [ 'http://xmlsoft.org/sources/', @@ -18,6 +18,6 @@ sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' -dependencies = [('zlib', '1.2.7')] +dependencies = [('zlib', '1.2.8')] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb similarity index 90% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb rename to easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb index 4fc4a74955..52ee0616b0 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb @@ -8,7 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" -toolchain = {'name': 'GCC', 'version': '4.8.2'} +toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [ 'http://xmlsoft.org/sources/', diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb deleted file mode 100644 index a6b6f7f14b..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.6.3.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.7' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'GCC', 'version': '4.6.3'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb deleted file mode 100644 index f2216d86e1..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.2.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.7' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'GCC', 'version': '4.7.2'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb deleted file mode 100644 index 572b633565..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-GCC-4.7.3.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.7' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'GCC', 'version': '4.7.3'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb deleted file mode 100644 index 1a28c0fbf0..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.8' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, -not covered by any patents -- lossless data-compression library for use on virtually any -computer hardware and operating system.""" - -toolchain = {'name': 'GCC', 'version': '4.8.3'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' -- GitLab From 783e26182242e9460fc377a6cd283a6c4f1b8424 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 12:51:04 +0200 Subject: [PATCH 680/992] fix toolchain for libxml2 dep in GLib intel/2015a easyconfig --- easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb index aa417b69e0..7f0fde608b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb @@ -16,7 +16,7 @@ dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), ('libxml2', '2.9.2'), - ('libxml2', '2.9.2', '', ('GCC', '4.9.2')), + ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] -- GitLab From 321625a11a897eecf2e9f62132af536b76fb8d06 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 13:01:31 +0200 Subject: [PATCH 681/992] use older libxml2 version in GLib easyconfigs using old toolchain (for compatibility with existing DOLFIN easyconfigs) --- easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb index 810a19f768..db0b390028 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1'), + ('libxml2', '2.8.0'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb index 767bcb84db..faced55c2c 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goolf-1.4.10.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1'), + ('libxml2', '2.8.0'), ] builddependencies = [('Python', '2.5.6', '-bare')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb index 1aa508846f..3b25385b1f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb @@ -15,7 +15,7 @@ sources = ['glib-%(version)s.tar.xz'] dependencies = [ ('libffi', '3.0.13'), ('gettext', '0.18.2'), - ('libxml2', '2.9.1'), + ('libxml2', '2.8.0'), ] builddependencies = [('Python', '2.5.6', '-bare')] -- GitLab From 6dab59bc0d473da361da1a6c61a060a67d1bc3a6 Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Thu, 4 Jun 2015 13:35:37 +0200 Subject: [PATCH 682/992] - SOBAcl-r18-intel-2014b-Perl-5.20.0.eb : added EasyConfig for SOBAcl --- .../SOBAcl-r18-intel-2014b-Perl-5.20.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb diff --git a/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000..e58e9e902a --- /dev/null +++ b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,22 @@ +easyblock = "Tarball" + +name = 'SOBAcl' +version = 'r18' + +homepage = 'http://www.sequenceontology.org/software/sobacl.html' +description = """SOBAcl is a command line tool for analyzing GFF3 annotations. +GFF3 is a standard file format for genomic annotation data. SOBAcl gathers +statistics from GFF3 files and can generate a wide variety of tables +and graphs.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +sources = [('SOBA_%s.tar.gz' % (version))] +source_urls = ['http://www.sequenceontology.org/software/SOBA_Code/'] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [('GraphViz', '2.18', versionsuffix)] + +moduleclass = 'bio' -- GitLab From 784b9e81f1b93f257288eacc06378402e162e60f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 13:36:42 +0200 Subject: [PATCH 683/992] fix double dep --- easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb index 7f0fde608b..8cf2990d69 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-foss-2015a.eb @@ -16,7 +16,6 @@ dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), ('libxml2', '2.9.2'), - ('libxml2', '2.9.2'), ] builddependencies = [('Python', '2.7.9')] -- GitLab From 96abaf33719fac2b1fdb38a6a8fca7597562eb73 Mon Sep 17 00:00:00 2001 From: CalcUA Core Facility Date: Thu, 4 Jun 2015 13:48:59 +0200 Subject: [PATCH 684/992] - moved file --- .../GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{Graphviz => }/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb (100%) diff --git a/easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb similarity index 100% rename from easybuild/easyconfigs/g/Graphviz/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb rename to easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb -- GitLab From bd80a031d510a0c2343980e760473a1271ee4dd0 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Thu, 4 Jun 2015 15:12:49 +0200 Subject: [PATCH 685/992] - changed source_urls and homepage --- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb | 6 +++--- .../easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb | 7 +++++-- easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb | 6 +++--- easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb | 6 +++--- 13 files changed, 41 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb index feb10d4a75..b6405c19b6 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb index e8472dac11..54ce3a5791 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb index c489c5aa68..7ff79c377b 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb index 4a7a10534b..327564fbd3 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb @@ -1,15 +1,15 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'lowopt': True} # use -O1 source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb index a411477c0b..1bfd983e7e 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb index 3c0ae0a9af..3644b946c0 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb index 7569a7cd7b..6abe0d811d 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb index d39e90c9e4..7bcfcdfee8 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb @@ -1,12 +1,15 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} -source_urls = ['http://download.qt-project.org/official_releases/qt/4.8/4.8.5/'] +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb index 312d6b1990..bfd0e1cd2f 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb index 2111ce217a..0bfab5d015 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'foss', 'version': '2015a'} source_urls = [ - 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/', - 'http://master.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb index 6435694c00..a829af981d 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb index 1c0c56d935..61b425c25a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb index aa253ef5eb..7ca9946d90 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2015a'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -- GitLab From c5305829749516f37ebc83fbfebed7c0a519c298 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 19:00:46 +0200 Subject: [PATCH 686/992] include comment in patch file --- .../easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch index eef94268d9..ba79adb02e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch @@ -1,3 +1,5 @@ +replace svnversion call with mimiced output for non-SVN tarballs for older versions of svnversion, i.e 'exported' +author: Kenneth Hoste (Ghent University) --- Python-2.5.6/configure.orig 2015-04-29 10:40:05.254502098 +0200 +++ Python-2.5.6/configure 2015-04-29 10:42:01.739388944 +0200 @@ -4242,7 +4242,8 @@ -- GitLab From 04720cdff35327efe1f76b18add69f54fcafb678 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jun 2015 20:24:47 +0200 Subject: [PATCH 687/992] fix patches redefinition in Python 2.5.6 ictce/4.x easyconfigs --- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 7 ++++--- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index 5cad1244b7..23ddabe854 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -11,9 +11,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['Python-%(version)s_svnversion-cmd.patch'] - -patches = ['python_libffi_int128_icc.patch'] +patches = [ + 'python_libffi_int128_icc.patch', + 'Python-%(version)s_svnversion-cmd.patch', +] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index eecf1e2276..f747214b5c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -11,9 +11,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['Python-%(version)s_svnversion-cmd.patch'] - -patches = ['python_libffi_int128_icc.patch'] +patches = [ + 'python_libffi_int128_icc.patch', + 'Python-%(version)s_svnversion-cmd.patch', +] dependencies = [ ('bzip2', '1.0.6'), -- GitLab From 04f0dfd8c6c008bfe0662dc4405cdc3ac656b167 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Fri, 5 Jun 2015 00:23:06 +0200 Subject: [PATCH 688/992] - fixed typo in source_urls for SQL::Abstract --- easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb index afa1c420a1..c7d3a27ade 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb @@ -838,7 +838,7 @@ exts_list = [ }), ('SQL::Abstract', '1.81', { 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/S/'], + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/'], }), ('GD::Graph', '1.49', { 'source_tmpl': 'GDGraph-1.49.tar.gz', -- GitLab From 533e2e962832fc58cc5dc5bfa6ca5f59111d66f6 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 10:18:45 +0200 Subject: [PATCH 689/992] .eb file to install GenotypeHarmonizer version 1.4.14 with Java 1.7.0 --- ...GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb new file mode 100644 index 0000000000..153a9953dd --- /dev/null +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ + +name = 'GenotypeHarmonizer' +version = '1.4.14' + +homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer' +description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +easyblock = 'PackedBinary' + +dependencies = [('Java', '1.7.0_80')] + +# +# Example URL +# http://www.molgenis.org/downloads/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-dist.tar.gz +# +download_name = 'Genotype-Harmonizer' +source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] +sources = ['GenotypeHarmonizer-%s-dist.tar.gz' % version] + +checksums = ['0a7b041efdd7a5d7ced0ae48eb4a9e06'] #GenotypeHarmonizer-1.4.14-dist.tar.gz + +sanity_check_paths = { + 'files': ['GenotypeHarmonizer.jar', 'GenotypeHarmonizer.sh'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 086221427b3d2b1237def12ec15e26a673945a97 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 10:31:49 +0200 Subject: [PATCH 690/992] .eb file to install hisat 0.1.5 (beta) with goolf 1.7.20 --- .../h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb new file mode 100644 index 0000000000..ea115e16fb --- /dev/null +++ b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb @@ -0,0 +1,33 @@ + +name = 'hisat' +version = '0.1.5-beta' + +homepage = 'http://ccb.jhu.edu/software/hisat/index.shtml' +description = """ +HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, +HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic +region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) +combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. +The memory footprint of HISAT is relatively low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +easyblock = 'MakeCp' +# +# Example URL: +# http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.6-beta-source.zip +# +sources = ['%(name)s-%(version)s-source.zip'] +source_urls = ['http://ccb.jhu.edu/software/hisat/downloads/'] + +checksums = ['9524a0170d85c5b560b51e0087f4cf46'] # hisat-0.1.5-beta-source.zip + +executables = [name,'hisat-build','hisat-inspect','hisat-build-s','hisat-inspect-s','hisat-align-s','hisat-build-l','hisat-inspect-l','hisat-align-l'] +files_to_copy = [(executables, 'bin')] + + +sanity_check_paths = { + 'files': ['bin/%s' % name], + 'dirs': []} + +moduleclass = 'bio' -- GitLab From ff1a0123332cbaf59aebd7971891c749a9765a5b Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:12:31 +0200 Subject: [PATCH 691/992] Change formatting, remove unused variable, remove some coments --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 153a9953dd..73d9434519 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -1,3 +1,5 @@ +toolchain = {'name': 'dummy', 'version': 'dummy'} +easyblock = 'PackedBinary' name = 'GenotypeHarmonizer' version = '1.4.14' @@ -5,20 +7,12 @@ version = '1.4.14' homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer' description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} -easyblock = 'PackedBinary' - dependencies = [('Java', '1.7.0_80')] -# -# Example URL -# http://www.molgenis.org/downloads/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-dist.tar.gz -# -download_name = 'Genotype-Harmonizer' source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] -sources = ['GenotypeHarmonizer-%s-dist.tar.gz' % version] +sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] -checksums = ['0a7b041efdd7a5d7ced0ae48eb4a9e06'] #GenotypeHarmonizer-1.4.14-dist.tar.gz +checksums = ['0a7b041efdd7a5d7ced0ae48eb4a9e06'] sanity_check_paths = { 'files': ['GenotypeHarmonizer.jar', 'GenotypeHarmonizer.sh'], -- GitLab From 63bd74aac9f22eb3fb7a3e152394651ccdbba66d Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:16:26 +0200 Subject: [PATCH 692/992] Add Java suffix --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 73d9434519..6df1f25684 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -7,7 +7,10 @@ version = '1.4.14' homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer' description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" -dependencies = [('Java', '1.7.0_80')] +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] -- GitLab From 6aa287531834b83ed81614bc5e6a09ad1b4b9ca3 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:22:56 +0200 Subject: [PATCH 693/992] Change structure, remove unnecesarry comments, make lines max 120 char long --- .../h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb | 32 +++++++++---------- 1 file changed, 15 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb index ea115e16fb..259f21eb5b 100644 --- a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb @@ -1,33 +1,31 @@ +toolchain = {'name': 'goolf', 'version': '1.7.20'} +easyblock = 'MakeCp' name = 'hisat' version = '0.1.5-beta' homepage = 'http://ccb.jhu.edu/software/hisat/index.shtml' -description = """ -HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, -HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic -region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) -combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. -The memory footprint of HISAT is relatively low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index. """ +description = """HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one + global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover + the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the + human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective + alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively + low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the + operations on the FM index. """ -toolchain = {'name': 'goolf', 'version': '1.7.20'} - -easyblock = 'MakeCp' -# -# Example URL: -# http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.6-beta-source.zip -# sources = ['%(name)s-%(version)s-source.zip'] source_urls = ['http://ccb.jhu.edu/software/hisat/downloads/'] -checksums = ['9524a0170d85c5b560b51e0087f4cf46'] # hisat-0.1.5-beta-source.zip +checksums = ['9524a0170d85c5b560b51e0087f4cf46'] -executables = [name,'hisat-build','hisat-inspect','hisat-build-s','hisat-inspect-s','hisat-align-s','hisat-build-l','hisat-inspect-l','hisat-align-l'] +executables = [name, 'hisat-build', 'hisat-inspect', 'hisat-build-s', 'hisat-inspect-s', 'hisat-align-s', + 'hisat-build-l', 'hisat-inspect-l', 'hisat-align-l'] files_to_copy = [(executables, 'bin')] sanity_check_paths = { - 'files': ['bin/%s' % name], - 'dirs': []} + 'files': ['bin/%(name)s'], + 'dirs': [], +} moduleclass = 'bio' -- GitLab From cd8f2801e79a9efdb70b598679db62701096d0fa Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:43:03 +0200 Subject: [PATCH 694/992] .eb file to install veryifyBamID-1.1.2 with goolf 1.7.20 --- .../verifyBamID-1.1.2-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..a567543a99 --- /dev/null +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +toolchain = {'name': 'goolf', 'version': '1.7.20'} +easyblock = 'MakeCp' + +name = 'verifyBamID' +version = '1.1.2' + +homepage = "http://csg.sph.umich.edu/kang/verifyBamID/index.html" +description = """verifyBamID is a software that verifies whether the reads in particular file match previously known + genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of + two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When + external genotypes are not available, verifyBamID still robustly detects sample swaps. +""" + +source_urls = ['https://github.com/statgen/%(name)s/releases/download/v%(version)s'] +sources = ['%(name)sLibStatGen.%(version)s.tgz'] + +checksums = ['fafc6fa58ba2bd51d0324ae616f5b29e'] + +buildopts = 'CXX="$CXX"' + +executables = ['%(name)s/bin/%(name)s'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['bin'] +} + + +moduleclass = 'bio' -- GitLab From 419ef5a2e4ea30284b8dff41e15d7a2aaf1c58c3 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:47:13 +0200 Subject: [PATCH 695/992] move toolchain to correct position --- .../v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb index a567543a99..df27e86592 100644 --- a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb @@ -1,4 +1,3 @@ -toolchain = {'name': 'goolf', 'version': '1.7.20'} easyblock = 'MakeCp' name = 'verifyBamID' @@ -11,6 +10,8 @@ description = """verifyBamID is a software that verifies whether the reads in pa external genotypes are not available, verifyBamID still robustly detects sample swaps. """ +toolchain = {'name': 'goolf', 'version': '1.7.20'} + source_urls = ['https://github.com/statgen/%(name)s/releases/download/v%(version)s'] sources = ['%(name)sLibStatGen.%(version)s.tgz'] -- GitLab From dfc74d982c4b96b0b3ab4b636978b892b7600ea6 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 14:50:20 +0200 Subject: [PATCH 696/992] move toolchain to correct position of GenotypeHarmonizer --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 6df1f25684..ae8a4779c4 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -1,4 +1,3 @@ -toolchain = {'name': 'dummy', 'version': 'dummy'} easyblock = 'PackedBinary' name = 'GenotypeHarmonizer' @@ -12,6 +11,8 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] +toolchain = {'name': 'dummy', 'version': 'dummy'} + source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] -- GitLab From 04b6ed4336535e25724ba08e19a519be1ecfb236 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 14:59:26 +0200 Subject: [PATCH 697/992] Update GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 6df1f25684..e326971151 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -5,7 +5,8 @@ name = 'GenotypeHarmonizer' version = '1.4.14' homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer' -description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" +description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data + stored using different file formats with different and potentially unknown strands.""" java = 'Java' javaver = '1.7.0_80' -- GitLab From 3ee04bc72791a0240774684f74213bf48aac8996 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 5 Jun 2015 15:12:35 +0200 Subject: [PATCH 698/992] .eb file to install STAR-2.3.1z12 with goolf-1.7.20 --- .../s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb new file mode 100644 index 0000000000..b2877e3d85 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.3.1z12' + +homepage = 'https://code.google.com/p/rna-star/' +description = """STAR: ultrafast universal RNA-seq aligner""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/alexdobin/%(name)s/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +checksums = ['c1e5b36a02011a73f9461f5bdc4dacaa'] + +buildopts = 'CXX="$CXX"' + +executables = [name, 'STARstatic'] +files_to_copy = [(executables,'bin/')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['bin'] +} + +moduleclass = 'bio' -- GitLab From 036e4afe8fedd7841aa803b15f2de4e98e7178dc Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 15:56:50 +0200 Subject: [PATCH 699/992] Update GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index e326971151..0fa0ab2a82 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -1,4 +1,3 @@ -toolchain = {'name': 'dummy', 'version': 'dummy'} easyblock = 'PackedBinary' name = 'GenotypeHarmonizer' @@ -8,6 +7,8 @@ homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) -- GitLab From 8cd4a7666d4d2e04af1b4bd8aa588116395b1d67 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 15:58:15 +0200 Subject: [PATCH 700/992] Update hisat-0.1.5-beta-goolf-1.7.20.eb toolchain under description --- easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb index 259f21eb5b..bd8c70bf67 100644 --- a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb @@ -1,4 +1,3 @@ -toolchain = {'name': 'goolf', 'version': '1.7.20'} easyblock = 'MakeCp' name = 'hisat' @@ -13,6 +12,8 @@ description = """HISAT is a fast and sensitive spliced alignment program for map low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index. """ +toolchain = {'name': 'goolf', 'version': '1.7.20'} + sources = ['%(name)s-%(version)s-source.zip'] source_urls = ['http://ccb.jhu.edu/software/hisat/downloads/'] -- GitLab From 975d6dea145980a328419ef84003a32f08b31a1b Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 15:59:52 +0200 Subject: [PATCH 701/992] Empty dirs list, removed double whiteline --- .../v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb index df27e86592..1d1bbb0d8a 100644 --- a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb @@ -24,8 +24,7 @@ files_to_copy = [(executables, 'bin')] sanity_check_paths = { 'files': ['bin/%(name)s'], - 'dirs': ['bin'] + 'dirs': [] } - moduleclass = 'bio' -- GitLab From 5d83a5b480707abec4cb12456e9274751d46dd6f Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 16:01:35 +0200 Subject: [PATCH 702/992] Empty dirs list --- easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb index b2877e3d85..2a0cc25f41 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb @@ -20,7 +20,7 @@ files_to_copy = [(executables,'bin/')] sanity_check_paths = { 'files': ['bin/%(name)s'], - 'dirs': ['bin'] + 'dirs': [] } moduleclass = 'bio' -- GitLab From ac88a9ae60798533125e3ff733a09e7fbc2117d6 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 5 Jun 2015 16:02:16 +0200 Subject: [PATCH 703/992] Extra space after executables, removed trailing / --- easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb index 2a0cc25f41..01b05100cc 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb @@ -16,7 +16,7 @@ checksums = ['c1e5b36a02011a73f9461f5bdc4dacaa'] buildopts = 'CXX="$CXX"' executables = [name, 'STARstatic'] -files_to_copy = [(executables,'bin/')] +files_to_copy = [(executables, 'bin')] sanity_check_paths = { 'files': ['bin/%(name)s'], -- GitLab From 7ca80e3e4e7baded83582ec2cf48ae1a0d5e4fe3 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 5 Jun 2015 16:25:00 +0200 Subject: [PATCH 704/992] Adding the infiniband patch for OpenMPI --- .../openmpi-mca-params.conf-1.8.5-local.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch new file mode 100644 index 0000000000..f9fa71615a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch @@ -0,0 +1,12 @@ +--- opal/etc/openmpi-mca-params.conf.orig 2015-06-05 16:21:25.535727000 +0200 ++++ opal/etc/openmpi-mca-params.conf 2015-06-05 16:21:05.855302000 +0200 +@@ -56,3 +56,9 @@ + + # See "ompi_info --param all all" for a full listing of Open MPI MCA + # parameters available and their default values. ++ ++# FG, 20130317; customization for University of Luxembourg systems ++btl_openib_if_exclude=mlx4_1 ++btl_openib_warn_nonexistent_if=0 ++orte_rsh_agent=oarsh ++btl_openib_memalign_threshold=12288 -- GitLab From d48b8df51270d1475929665777186e33948b514b Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Mon, 8 Jun 2015 10:37:40 +0200 Subject: [PATCH 705/992] Updating patch file --- .../o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch index f9fa71615a..0d7989a781 100644 --- a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch +++ b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch @@ -1,12 +1,9 @@ --- opal/etc/openmpi-mca-params.conf.orig 2015-06-05 16:21:25.535727000 +0200 -+++ opal/etc/openmpi-mca-params.conf 2015-06-05 16:21:05.855302000 +0200 -@@ -56,3 +56,9 @@ ++++ opal/etc/openmpi-mca-params.conf 2015-06-08 10:36:05.387902000 +0200 +@@ -56,3 +56,6 @@ # See "ompi_info --param all all" for a full listing of Open MPI MCA # parameters available and their default values. + -+# FG, 20130317; customization for University of Luxembourg systems -+btl_openib_if_exclude=mlx4_1 -+btl_openib_warn_nonexistent_if=0 -+orte_rsh_agent=oarsh ++# Fix bug in the initialization of the value when using the infiniband module. (ref: http://www.open-mpi.org/community/lists/users/2015/05/26913.php) +btl_openib_memalign_threshold=12288 -- GitLab From 060dbaee4587aee036ed1edb18ce4336f0564715 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Mon, 8 Jun 2015 10:58:17 +0200 Subject: [PATCH 706/992] Adding patch to the easyconfigs --- .../o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 5 ++++- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 5 ++++- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 5 ++++- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 5 ++++- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 5 ++++- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 5 ++++- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 4 ++++ .../OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ++++ .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 5 +++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb | 4 ++++ .../OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ++++ .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 4 ++++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb | 4 ++++ .../o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 4 ++++ .../o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 4 ++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 4 ++++ ...5-local.patch => openmpi-mca-params.conf-pre-1.8.6.patch} | 0 27 files changed, 103 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/o/OpenMPI/{openmpi-mca-params.conf-1.8.5-local.patch => openmpi-mca-params.conf-pre-1.8.6.patch} (100%) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 3f5d4cafd7..8037292116 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -20,6 +20,10 @@ dependencies = [('hwloc', '1.6')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 68114cf721..4439183191 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 109447fa55..286b13e558 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 983eb22945..84ed520e49 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,6 +19,10 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 7d3922cea0..3f37ffe201 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 21bd882ac7..5c8698cf2a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,6 +24,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 90dc3e3449..0d4e8e1a10 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index 5e9b5fcda8..c52fa56a7c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 394c231617..0adf96e75a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 6cac76d97d..251f47e42c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 908f092bfa..ccd7bda9e9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index c9d45613df..cf9baf6195 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'GCC', 'version': '4.8.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 85b6644c9f..faf4a7a6d8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,6 +20,10 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 4d2c94f271..046590fd3c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,6 +18,10 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 79c31e1c3d..bb279bfe90 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,6 +20,10 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 1f4d38649b..d7b0f1bcd1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -23,6 +23,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index fdf4f47fc8..2dd1f2e385 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -11,9 +11,10 @@ toolchain = {'name': 'gcccuda', 'version': '2.6.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = [ +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-%(version)s_common-cuda-lib.patch', - 'OpenMPI-%(version)s-vt_cupti_events.patch' + 'OpenMPI-%(version)s-vt_cupti_events.patch', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index d9eca98720..881ad83275 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index fb7afbbd41..063c84b4a4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index e1057430c2..2bf0d5beb0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -20,6 +20,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.9')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index f73d19d32c..f4723656da 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -22,6 +22,10 @@ dependencies = [('hwloc', '1.9')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 3841ad29d2..df7fe4109e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index e90682df3b..6e2e0d1429 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index a3c918320f..d8a312b1ae 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -22,6 +22,10 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index d7df86c8d6..2e31a0bff5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -23,6 +23,10 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb index 17455567fb..275ab25d92 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -21,6 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +patches = [ + 'openmpi-mca-params.conf-pre-1.8.6.patch', +] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch similarity index 100% rename from easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.8.5-local.patch rename to easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch -- GitLab From 00fd39553d0fe8a0bdc8b3e882883ef486c490a6 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Mon, 8 Jun 2015 11:11:29 +0200 Subject: [PATCH 707/992] Removed duplicated toolchain line --- .../GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 47397c2963..0fa0ab2a82 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -14,8 +14,6 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -toolchain = {'name': 'dummy', 'version': 'dummy'} - source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] -- GitLab From 367008cd44fb4095ca264b9ed912d50525186d94 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 8 Jun 2015 12:28:24 +0200 Subject: [PATCH 708/992] Adjusted Qt homepage and download URL --- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb index e0d6a9d420..f353838078 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -- GitLab From 106f2e27f32ef0a8747644868154e4d0090c7540 Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 13:08:13 +0200 Subject: [PATCH 709/992] Add .eb files for snpEff v3.6 and snpEff v4.1d --- .../s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb | 31 +++++++++++++++++++ .../s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000..6278b4ba19 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb @@ -0,0 +1,31 @@ +import time + +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '3.6' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. +It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +seconds_after_epoch = int(time.time()) +source_urls = [('http://downloads.sourceforge.net/project/%s?ts=%s&use_mirror=autoselect' % (name.lower(), seconds_after_epoch))] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +checksums = ['f4571413833df913261ff76b6f40bb76'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb new file mode 100644 index 0000000000..7763b7baad --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb @@ -0,0 +1,31 @@ +import time + +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '4.1d' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. +It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +seconds_after_epoch = int(time.time()) +source_urls = ['http://downloads.sourceforge.net/project/%(name.lower())s?ts=%(seconds_after_epoch)s&use_mirror=autoselect'] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 485b56534fa1575183454ec91041b388ca61650b Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 13:30:09 +0200 Subject: [PATCH 710/992] .eb file for SAMtools 0.1.19 with goolf 1.7.20 --- .../SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb new file mode 100644 index 0000000000..ceb5083895 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb @@ -0,0 +1,23 @@ + +name = 'SAMtools' +version = '0.1.19' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +checksums = ['ff8b46e6096cfb452003b1ec5091d86a'] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' -- GitLab From 7cb1ac217609a76bfcd6121e84e1ad10eef6ca3e Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 13:42:50 +0200 Subject: [PATCH 711/992] .eb file for PLINK-1.07-x86_64-goolf-1.7.20 --- .../p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb new file mode 100644 index 0000000000..aa31391d7e --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.07-x86_64' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = "plink-1.07-src: Whole-genome association analysis toolset" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s-%(version)s.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +checksums = ['fd0bafeda42151b20534e4f97b0d97df'] + +files_to_copy = [ + "plink", + "gPLINK.jar", + "test.map", + "test.ped", + "COPYING.txt", + "README.txt", +] + +sanity_check_paths = { + 'files': ["plink", "gPLINK.jar", "test.map", "test.ped", "COPYING.txt", "README.txt"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0c3e759c7413dfee31b4dcb1e8f30cac7719b82b Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 13:45:45 +0200 Subject: [PATCH 712/992] changed double quotes to single quotes to conform with other .eb files --- .../p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb index aa31391d7e..50bb76fbb3 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb @@ -4,7 +4,7 @@ name = 'PLINK' version = '1.07-x86_64' homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' -description = "plink-1.07-src: Whole-genome association analysis toolset" +description = 'plink-1.07-src: Whole-genome association analysis toolset' toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -14,16 +14,16 @@ source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] checksums = ['fd0bafeda42151b20534e4f97b0d97df'] files_to_copy = [ - "plink", - "gPLINK.jar", - "test.map", - "test.ped", - "COPYING.txt", - "README.txt", + 'plink', + 'gPLINK.jar', + 'test.map', + 'test.ped', + 'COPYING.txt', + 'README.txt', ] sanity_check_paths = { - 'files': ["plink", "gPLINK.jar", "test.map", "test.ped", "COPYING.txt", "README.txt"], + 'files': ['plink', 'gPLINK.jar', 'test.map', 'test.ped', 'COPYING.txt', 'README.txt'], 'dirs': [], } -- GitLab From 83ebc81820da3cba5d24fff87a4bcbc8398ec073 Mon Sep 17 00:00:00 2001 From: npklein Date: Mon, 8 Jun 2015 14:59:23 +0200 Subject: [PATCH 713/992] Change name of .eb file because it is already compiled (so goolf not used) --- .../easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb new file mode 100644 index 0000000000..50bb76fbb3 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.07-x86_64' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = 'plink-1.07-src: Whole-genome association analysis toolset' + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s-%(version)s.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +checksums = ['fd0bafeda42151b20534e4f97b0d97df'] + +files_to_copy = [ + 'plink', + 'gPLINK.jar', + 'test.map', + 'test.ped', + 'COPYING.txt', + 'README.txt', +] + +sanity_check_paths = { + 'files': ['plink', 'gPLINK.jar', 'test.map', 'test.ped', 'COPYING.txt', 'README.txt'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From f15b0f5792fba76b9644b0f36fe899ffc1538017 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Mon, 8 Jun 2015 15:12:44 +0200 Subject: [PATCH 714/992] Delete PLINK-1.07-x86_64-goolf-1.7.20.eb --- .../p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb deleted file mode 100644 index 50bb76fbb3..0000000000 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64-goolf-1.7.20.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'PLINK' -version = '1.07-x86_64' - -homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' -description = 'plink-1.07-src: Whole-genome association analysis toolset' - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['%(namelower)s-%(version)s.zip'] -source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] - -checksums = ['fd0bafeda42151b20534e4f97b0d97df'] - -files_to_copy = [ - 'plink', - 'gPLINK.jar', - 'test.map', - 'test.ped', - 'COPYING.txt', - 'README.txt', -] - -sanity_check_paths = { - 'files': ['plink', 'gPLINK.jar', 'test.map', 'test.ped', 'COPYING.txt', 'README.txt'], - 'dirs': [], -} - -moduleclass = 'bio' -- GitLab From 918acfe57a9bc8d53cf9e38eb0df549dbc632336 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 3 Jun 2015 13:15:57 +0200 Subject: [PATCH 715/992] Add support for R pbd. --- ...bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 45 +++++++++++++++++++ ..._ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb create mode 100644 easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb new file mode 100644 index 0000000000..05e79faaa5 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'R-bundle' +version = '20150605' +bundlename = 'pbd' +rver = '3.1.3' +versionsuffix = '-R-%s-%s' % (rver, bundlename) + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('pbdMPI', '0.2-5', ext_options), + ('pbdSLAP', '0.2-0', ext_options), + ('pbdBASE', '0.2-3', dict(ext_options.items() + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), + ('pbdDMAT', '0.2-3', ext_options), + ('pbdDEMO', '0.2-0', ext_options), + ('pmclust', '0.1-6', ext_options), + ('EMCluster', '0.2-4', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch new file mode 100644 index 0000000000..ae54615b78 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch @@ -0,0 +1,45 @@ +# Add support for intel mpi by removing references to BI_COMM_WORLD +# BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. +--- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 ++++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 +@@ -25,7 +25,9 @@ + BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; + BLACS_APTS.BI_MyContxts = BI_MyContxts; + BLACS_APTS.BI_SysContxts = BI_SysContxts; ++#ifndef __INTEL_COMPILER + BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; ++#endif + BLACS_APTS.BI_Stats = BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -44,7 +46,9 @@ + BI_AuxBuff.nAops, BI_AuxBuff.N); + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); ++#ifndef __INTEL_COMPILER + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#endif + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); +@@ -89,7 +93,9 @@ + + BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; + BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; ++#ifndef __INTEL_COMPILER + BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; ++#endif + BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -109,7 +115,9 @@ + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#ifndef __INTEL_COMPILER + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); ++#endif + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); + } + -- GitLab From 56c5d760efd84b2fd311b99289b3f154caf0a638 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 15:04:48 +0200 Subject: [PATCH 716/992] Updated PDT easyconfigs - removed config parameter hackery now taken care of by custom easyblock - add checksums --- .../p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb | 36 +++++-------------- .../easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb | 36 +++++-------------- .../easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb | 35 +++++------------- 3 files changed, 27 insertions(+), 80 deletions(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb index a6ab7c4155..eef9a27cd7 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.19" @@ -20,31 +22,11 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -skipsteps = ['build'] - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb index 7faa216ef2..f50e7519a2 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.19" @@ -20,31 +22,11 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'ictce', 'version': '5.3.0'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -skipsteps = ['build'] - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb index 124698a037..4acb86b021 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.20" @@ -23,27 +25,8 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -skipsteps = ['build'] - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + 'c3edabe202926abe04552e33cd39672d', # pdtoolkit-3.20.tar.gz +] moduleclass = 'perf' -- GitLab From 7943c8d70acbe73e7c67da54dcc235e25625ae57 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 17:03:35 +0200 Subject: [PATCH 717/992] Update to latest Vampir release, adding suggested parameters for silent installation --- ...x-x86_64.eb => Vampir-8.4.1-foss-2015a.eb} | 24 ++++++++++++------- 1 file changed, 16 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.1.0-linux-x86_64.eb => Vampir-8.4.1-foss-2015a.eb} (54%) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb similarity index 54% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 7b467d1272..51ba49a2a0 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.1.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -1,16 +1,17 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## easyblock='Binary' name = "Vampir" -version = "8.1.0" -versionsuffix = "-linux-x86_64" +version = "8.4.1" homepage = 'http://www.vampir.eu' description = """The VAMPIR software tool provides an easy-to-use framework that enables @@ -18,15 +19,22 @@ description = """The VAMPIR software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'foss', 'version': '2015a'} -sources = ['vampir-%(version)s-standard%(versionsuffix)s-setup.bin'] +sources = ['vampir-%s-linux-x86_64-setup.bin' % (version)] -install_cmd = "./vampir-%(version)s-standard%(versionsuffix)s-setup.bin --silent --instdir=%(installdir)s" +install_cmd = "./vampir-8.4.1-linux-x86_64-setup.bin --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], 'dirs': [] } +# Adjust this variable to point to the location of your Vampir license file +license_file = '/opt/local/licenses/vampir.license' + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + moduleclass = 'perf' -- GitLab From 8a2ca653eef8ef14c4b8e78af2ed75ca255b6bd6 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 17:04:57 +0200 Subject: [PATCH 718/992] Add corresponding easyconfig for VampirServer --- .../VampirServer-8.4.1-foss-2015a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb new file mode 100644 index 0000000000..2c7fb3e4eb --- /dev/null +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock='Binary' + +name = "VampirServer" +version = "8.4.1" + +homepage = 'http://www.vampir.eu' +description = """The VAMPIR software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +sources = ['vampirserver-%s-linux-x86_64-setup.bin' % (version)] + +install_cmd = "./vampirserver-8.4.1-linux-x86_64-setup.bin --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" + +sanity_check_paths = { + 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"], + 'dirs': [] +} + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/opt/local/licenses/vampir.license' + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' -- GitLab From 654d988b7ce03021f8964724e2a0c660f1899c4d Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 17:09:54 +0200 Subject: [PATCH 719/992] Use %(version)s where necessary --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 4 ++-- .../v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 51ba49a2a0..672d33cf47 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -21,9 +21,9 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'foss', 'version': '2015a'} -sources = ['vampir-%s-linux-x86_64-setup.bin' % (version)] +sources = ['vampir-%(version)s-linux-x86_64-setup.bin'] -install_cmd = "./vampir-8.4.1-linux-x86_64-setup.bin --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" +install_cmd = "./vampir-%(version)s-linux-x86_64-setup.bin --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index 2c7fb3e4eb..eb02b99c8b 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -22,9 +22,9 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {"usempi": True} -sources = ['vampirserver-%s-linux-x86_64-setup.bin' % (version)] +sources = ['vampirserver-%(version)s-linux-x86_64-setup.bin'] -install_cmd = "./vampirserver-8.4.1-linux-x86_64-setup.bin --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" +install_cmd = "./vampirserver-%(version)s-linux-x86_64-setup.bin --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"], -- GitLab From b277923e88621566d616ed3dd0a5f219a7d32bf7 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 19:54:10 +0200 Subject: [PATCH 720/992] Apply change to install_cmd as requested by review --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 3 ++- .../v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 672d33cf47..0c1ff46f1b 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -8,6 +8,7 @@ # This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock='Binary' name = "Vampir" @@ -23,7 +24,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['vampir-%(version)s-linux-x86_64-setup.bin'] -install_cmd = "./vampir-%(version)s-linux-x86_64-setup.bin --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { 'files': ["bin/vampir", "doc/vampir-manual.pdf"], diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index eb02b99c8b..f55fa79b0b 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -8,6 +8,7 @@ # This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock='Binary' name = "VampirServer" @@ -24,7 +25,7 @@ toolchainopts = {"usempi": True} sources = ['vampirserver-%(version)s-linux-x86_64-setup.bin'] -install_cmd = "./vampirserver-%(version)s-linux-x86_64-setup.bin --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"], -- GitLab From b63db539c28c29ab02c28b7e43f445c4555ab043 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 10 Jun 2015 20:00:53 +0200 Subject: [PATCH 721/992] Add checksums --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 4 ++++ .../v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 0c1ff46f1b..5328137af1 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -24,6 +24,10 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['vampir-%(version)s-linux-x86_64-setup.bin'] +checksums = [ + '471840910cd552a5a788df3b69251d29', # vampir-8.4.1-linux-x86_64-setup.bin +] + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index f55fa79b0b..4b737a9b8d 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -25,6 +25,10 @@ toolchainopts = {"usempi": True} sources = ['vampirserver-%(version)s-linux-x86_64-setup.bin'] +checksums = [ + '2a2236bb071168b7d488c83363c30ac8', # vampirserver-8.4.1-linux-x86_64-setup.bin +] + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { -- GitLab From 9c9bc2d63429032d4af4cf9be996c28ea9d27465 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 09:29:01 +0200 Subject: [PATCH 722/992] Added myself as an author --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 1 + .../easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index 5328137af1..2b1dcd0556 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -3,6 +3,7 @@ # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr +# Markus Geimer # License:: 3-clause BSD # # This work is based on experiences from the UNITE project diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index 4b737a9b8d..3710da1f32 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -3,6 +3,7 @@ # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr +# Markus Geimer # License:: 3-clause BSD # # This work is based on experiences from the UNITE project -- GitLab From 172f958d843229eb901ab5dac0b48cfd6bc0e86e Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 09:30:59 +0200 Subject: [PATCH 723/992] Renamed files to reflect supported platform --- ....4.1-foss-2015a.eb => Vampir-8.4.1-linux-x86_64-foss-2015a.eb} | 0 ...oss-2015a.eb => VampirServer-8.4.1-linux-x86_64-foss-2015a.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-foss-2015a.eb => Vampir-8.4.1-linux-x86_64-foss-2015a.eb} (100%) rename easybuild/easyconfigs/v/VampirServer/{VampirServer-8.4.1-foss-2015a.eb => VampirServer-8.4.1-linux-x86_64-foss-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb rename to easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb -- GitLab From bb8bba996ec6cd549de236a7e686624198f51de3 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 09:44:02 +0200 Subject: [PATCH 724/992] Make variant easily configurable --- .../v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb | 3 ++- .../VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb index 2b1dcd0556..b4541a5784 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb @@ -14,6 +14,7 @@ easyblock='Binary' name = "Vampir" version = "8.4.1" +variant = "linux-x86_64" homepage = 'http://www.vampir.eu' description = """The VAMPIR software tool provides an easy-to-use framework that enables @@ -23,7 +24,7 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'foss', 'version': '2015a'} -sources = ['vampir-%(version)s-linux-x86_64-setup.bin'] +sources = ['vampir-%s-%s-setup.bin' % (version, variant)] checksums = [ '471840910cd552a5a788df3b69251d29', # vampir-8.4.1-linux-x86_64-setup.bin diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb index 3710da1f32..472f9c6a46 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb @@ -14,6 +14,7 @@ easyblock='Binary' name = "VampirServer" version = "8.4.1" +variant = "linux-x86_64" homepage = 'http://www.vampir.eu' description = """The VAMPIR software tool provides an easy-to-use framework that enables @@ -24,7 +25,7 @@ description = """The VAMPIR software tool provides an easy-to-use framework that toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {"usempi": True} -sources = ['vampirserver-%(version)s-linux-x86_64-setup.bin'] +sources = ['vampirserver-%s-%s-setup.bin' % (version, variant)] checksums = [ '2a2236bb071168b7d488c83363c30ac8', # vampirserver-8.4.1-linux-x86_64-setup.bin -- GitLab From fe5b11b6e66289c17d4c7c01bf679d5879e2c740 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 09:59:50 +0200 Subject: [PATCH 725/992] Add easyconfig for Vampir demo version --- ...mpir-8.4.1-demo-linux-x86_64-foss-2015a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb new file mode 100644 index 0000000000..f6afd9c0a1 --- /dev/null +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb @@ -0,0 +1,48 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock='Binary' + +name = "Vampir" +version = "8.4.1" +versionsuffix = "-demo" +variant = "linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The VAMPIR software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] + +checksums = [ + '09cf28650be36516613372c8a0d1c0d8', # vampir-8.4.1-demo-linux-x86_64-setup.bin +] + +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" + +sanity_check_paths = { + 'files': ["bin/vampir", "doc/vampir-manual.pdf"], + 'dirs': [] +} + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/opt/local/licenses/vampir.license' + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' -- GitLab From 46fc4a3221648c5eb50726c2345b561374ebf41f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 10:35:26 +0200 Subject: [PATCH 726/992] Modify the example license_file value as suggested --- .../v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb | 2 +- .../v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb | 2 +- .../VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb index f6afd9c0a1..42c77ab311 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb @@ -39,7 +39,7 @@ sanity_check_paths = { } # Adjust this variable to point to the location of your Vampir license file -license_file = '/opt/local/licenses/vampir.license' +license_file = '/example/licenses/path/vampir.license' modextravars = { 'VAMPIR_LICENSE': license_file, diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb index b4541a5784..ffb4fc26ad 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb @@ -38,7 +38,7 @@ sanity_check_paths = { } # Adjust this variable to point to the location of your Vampir license file -license_file = '/opt/local/licenses/vampir.license' +license_file = '/example/licenses/path/vampir.license' modextravars = { 'VAMPIR_LICENSE': license_file, diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb index 472f9c6a46..83d53b0104 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb @@ -39,7 +39,7 @@ sanity_check_paths = { } # Adjust this variable to point to the location of your Vampir license file -license_file = '/opt/local/licenses/vampir.license' +license_file = '/example/licenses/path/vampir.license' modextravars = { 'VAMPIR_LICENSE': license_file, -- GitLab From 6f94a296a50a8952763305db3f376d6aad24f0a9 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 11 Jun 2015 10:36:53 +0200 Subject: [PATCH 727/992] Remove variant from file name due to EB policy/limitation --- ...linux-x86_64-foss-2015a.eb => Vampir-8.4.1-demo-foss-2015a.eb} | 0 ....4.1-linux-x86_64-foss-2015a.eb => Vampir-8.4.1-foss-2015a.eb} | 0 ...inux-x86_64-foss-2015a.eb => VampirServer-8.4.1-foss-2015a.eb} | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb => Vampir-8.4.1-demo-foss-2015a.eb} (100%) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-linux-x86_64-foss-2015a.eb => Vampir-8.4.1-foss-2015a.eb} (100%) rename easybuild/easyconfigs/v/VampirServer/{VampirServer-8.4.1-linux-x86_64-foss-2015a.eb => VampirServer-8.4.1-foss-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-linux-x86_64-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-linux-x86_64-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-linux-x86_64-foss-2015a.eb rename to easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb -- GitLab From ab60fa01e32da8f2bb3dbe45e7db4cfaf3e242b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 13:26:33 +0200 Subject: [PATCH 728/992] add custom sanity_check_paths in libxml2 easyconfigs --- .../libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb | 5 +++++ .../l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb | 5 +++++ .../l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 9 +++++++-- .../easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb | 5 +++++ .../l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb | 5 +++++ .../easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb | 5 +++++ 35 files changed, 177 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index aaf4c869fd..254704e224 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb index c67963ba18..3d078ed6cf 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb index d6a8666d27..33c6ee44e2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb @@ -23,4 +23,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb index 3d1f3f2077..d35a5afd09 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb @@ -18,4 +18,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb index ddf8c95989..2cbd068791 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb index c92bb71719..111dd07ee9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb index e56d2ad353..2e200ff747 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb index e014507e31..2e16511fc4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb index 1a06b1ab67..8718a3c0cd 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb index 833381d4b2..dd8fbb563c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb index 1babda58a0..5f8aa9158f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb index 9c2538dce1..df4be8cc11 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb @@ -18,4 +18,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb index 34aa5f2ec6..ddb04fedc9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb index 59de5c01a7..2d7551a78a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb index 5618053aba..f6b392b5e3 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb index 4f35163694..528265c88b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb index 0d54f03977..d743e7f4c4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb index 2145f1ccf3..824084e03a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index 6e4ab86218..96f39c944c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -4,8 +4,8 @@ name = 'libxml2' version = '2.9.1' homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable -outside of the Gnome platform).""" +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb index b46d67c8c8..35fadff4ea 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb index 42fd9996e9..a36d6bdb32 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb index 02c5f8e418..51cf5a1ff9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb index b3eac90a51..28520b4f81 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb index 232c2e480f..0c0ab111ee 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb index e18bbcef3b..d80e534ea6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb index ef442f4bb5..69506204a7 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb index 5c7f304740..69319cf49a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb index 3194637d11..cd4bbd99a0 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb index 102c2914db..3a42235cf9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb index 25967be117..d446d4e3c6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb index 12454bc9c4..fa340e7e85 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb index e2bb547666..ae74326843 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb index aae9d0148e..94f3df39be 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb index 52ee0616b0..215198c95a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb index 84a2d133c6..2857dd4e54 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' -- GitLab From f77fea64168d7dce85538313dffb5523bc7a257c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 15:14:10 +0200 Subject: [PATCH 729/992] {tools}[dummy] GC3Pie 2.2.3 --- easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb | 19 +++++++++++ .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 32 +++++++++++++++++++ .../p/PrettyTable/PrettyTable-0.7.2.eb | 20 ++++++++++++ .../easyconfigs/p/paramiko/paramiko-1.15.2.eb | 24 ++++++++++++++ .../p/parsedatetime/parsedatetime-1.4.eb | 19 +++++++++++ .../easyconfigs/p/pyCLI/pyCLI-20140329.eb | 22 +++++++++++++ .../easyconfigs/p/pycrypto/pycrypto-2.6.1.eb | 29 +++++++++++++++++ .../s/SQLAlchemy/SQLAlchemy-1.0.5.eb | 19 +++++++++++ 8 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb create mode 100644 easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb create mode 100644 easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb create mode 100644 easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb create mode 100644 easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb create mode 100644 easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb create mode 100644 easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb diff --git a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb new file mode 100644 index 0000000000..f6f2a181c2 --- /dev/null +++ b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'ecdsa' +version = '0.13' + +homepage = 'http://github.com/warner/python-ecdsa' +description = """ECDSA cryptographic signature library (pure Python).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/ecdsa'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb new file mode 100644 index 0000000000..cfeb39d2cd --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -0,0 +1,32 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'GC3Pie' +version = '2.2.3' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('ecdsa', '0.13'), # required for paramiko + ('pycrypto', '2.6.1'), # required for paramiko + ('paramiko', '1.15.2'), + ('PrettyTable', '0.7.2'), + ('pyCLI', '20140329'), + ('SQLAlchemy', '1.0.5'), + ('parsedatetime', '1.4'), +] + +options = {'modulename': 'gc3libs'} + +sanity_check_paths = { + 'files': ['bin/gc3utils'], + 'dirs': ['lib/gc3utils', 'lib/gc3libs'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb b/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb new file mode 100644 index 0000000000..a75ea18716 --- /dev/null +++ b/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb @@ -0,0 +1,20 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'PrettyTable' +version = '0.7.2' + +homepage = 'http://code.google.com/p/prettytable/' +description = """PrettyTable is a simple Python library designed to make it quick and easy to represent tabular data + in visually appealing ASCII tables.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/prettytable.py'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb b/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb new file mode 100644 index 0000000000..fb4a02667b --- /dev/null +++ b/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb @@ -0,0 +1,24 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'paramiko' +version = '1.15.2' + +homepage = 'https://github.com/paramiko/paramiko/' +description = """Native Python SSHv2 protocol library""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('ecdsa', '0.13'), + ('pycrypto', '2.6.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/paramiko'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb new file mode 100644 index 0000000000..181df165c0 --- /dev/null +++ b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'parsedatetime' +version = '1.4' + +homepage = 'http://github.com/bear/parsedatetime/' +description = """Parse human-readable date/time text.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/parsedatetime'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb b/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb new file mode 100644 index 0000000000..8c1d8067dd --- /dev/null +++ b/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb @@ -0,0 +1,22 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'pyCLI' +version = '20140329' + +homepage = 'http://packages.python.org/pyCLI/' +description = """Simple, object-oriented approach to Python CLI apps""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = ['pyCLI-devel.tar.gz'] +checksums = ['5cad880168f3423a1235b396735c1360'] + +options = {'modulename': 'cli'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/cli'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb b/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb new file mode 100644 index 0000000000..88292f1478 --- /dev/null +++ b/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pycrypto' +version = '2.6.1' + +homepage = 'http://www.pycrypto.org/' +description = """Cryptographic modules for Python.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# install into a path that's no specific to the Python version being used +installopts = '--install-lib=%(installdir)s/lib --no-compile' + +options = {'modulename': 'Crypto'} + +modextrapaths = {'PYTHONPATH': ['lib']} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/Crypto'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb new file mode 100644 index 0000000000..2354094058 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'SQLAlchemy' +version = '1.0.5' + +homepage = 'http://www.sqlalchemy.org/' +description = """Database Abstraction Library - The Python SQL Toolkit and Object Relational Mapper""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/sqlalchemy'], +} + +moduleclass = 'lib' -- GitLab From 6e151e945a3e87f9cc1a946a338675d617634d2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jun 2015 21:17:40 +0200 Subject: [PATCH 730/992] {devel}[GNU-5.1.0-2.25] Autotools 20150215 --- .../Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb | 26 +++++++++++++++ .../Automake/Automake-1.15-GNU-5.1.0-2.25.eb | 33 +++++++++++++++++++ .../Autotools-20150215-GNU-5.1.0-2.25.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb | 17 ++++++++++ .../m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb | 23 +++++++++++++ 5 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..af0a90aedb --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..1d63ee839d --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..0d6c26a78c --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..33c6f3867e --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000..e83b261924 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 69aefc331dd9bc2155c132b6ee81eed5819c2c55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 14 Jun 2015 01:41:50 +0200 Subject: [PATCH 731/992] fix GC3Pie dependencies, add sanity check command --- .../easyconfigs/a/argparse/argparse-1.3.0.eb | 19 +++++++++++ easybuild/easyconfigs/b/Babel/Babel-1.3.eb | 21 ++++++++++++ easybuild/easyconfigs/b/boto/boto-2.9.4.eb | 19 +++++++++++ .../e/ecdsa/{ecdsa-0.13.eb => ecdsa-0.11.eb} | 10 ++++-- .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 22 +++++++++---- .../easyconfigs/i/iso8601/iso8601-0.1.10.eb | 19 +++++++++++ ...{paramiko-1.15.2.eb => paramiko-1.13.0.eb} | 6 ++-- ...datetime-1.4.eb => parsedatetime-0.8.7.eb} | 2 +- easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb | 21 ++++++++++++ easybuild/easyconfigs/p/pip/pip-7.0.3.eb | 19 +++++++++++ .../{pyCLI-20140329.eb => pyCLI-2.0.3.eb} | 5 ++- .../python-novaclient-2.15.0.eb | 32 +++++++++++++++++++ easybuild/easyconfigs/p/pytz/pytz-2015.4.eb | 19 +++++++++++ .../easyconfigs/r/requests/requests-2.4.2.eb | 19 +++++++++++ ...QLAlchemy-1.0.5.eb => SQLAlchemy-0.7.9.eb} | 2 +- .../s/setuptools/setuptools-17.1.1.eb | 19 +++++++++++ .../s/simplejson/simplejson-3.7.3.eb | 19 +++++++++++ easybuild/easyconfigs/s/six/six-1.9.0.eb | 19 +++++++++++ 18 files changed, 276 insertions(+), 16 deletions(-) create mode 100644 easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb create mode 100644 easybuild/easyconfigs/b/Babel/Babel-1.3.eb create mode 100644 easybuild/easyconfigs/b/boto/boto-2.9.4.eb rename easybuild/easyconfigs/e/ecdsa/{ecdsa-0.13.eb => ecdsa-0.11.eb} (55%) create mode 100644 easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb rename easybuild/easyconfigs/p/paramiko/{paramiko-1.15.2.eb => paramiko-1.13.0.eb} (79%) rename easybuild/easyconfigs/p/parsedatetime/{parsedatetime-1.4.eb => parsedatetime-0.8.7.eb} (95%) create mode 100644 easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb create mode 100644 easybuild/easyconfigs/p/pip/pip-7.0.3.eb rename easybuild/easyconfigs/p/pyCLI/{pyCLI-20140329.eb => pyCLI-2.0.3.eb} (78%) create mode 100644 easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb create mode 100644 easybuild/easyconfigs/p/pytz/pytz-2015.4.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.4.2.eb rename easybuild/easyconfigs/s/SQLAlchemy/{SQLAlchemy-1.0.5.eb => SQLAlchemy-0.7.9.eb} (95%) create mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb create mode 100644 easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb create mode 100644 easybuild/easyconfigs/s/six/six-1.9.0.eb diff --git a/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb b/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb new file mode 100644 index 0000000000..6200884242 --- /dev/null +++ b/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'argparse' +version = '1.3.0' + +homepage = 'http://code.google.com/p/argparse/' +description = """Python command-line parsing library""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/argparse.py'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Babel/Babel-1.3.eb b/easybuild/easyconfigs/b/Babel/Babel-1.3.eb new file mode 100644 index 0000000000..916af760ce --- /dev/null +++ b/easybuild/easyconfigs/b/Babel/Babel-1.3.eb @@ -0,0 +1,21 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'Babel' +version = '1.3' + +homepage = 'http://babel.pocoo.org/' +description = """A collection of tools for internationalizing Python applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('pytz', '2015.4')] + +sanity_check_paths = { + 'files': ['bin/pybabel'], + 'dirs': ['lib/babel'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/boto/boto-2.9.4.eb b/easybuild/easyconfigs/b/boto/boto-2.9.4.eb new file mode 100644 index 0000000000..bec02fba24 --- /dev/null +++ b/easybuild/easyconfigs/b/boto/boto-2.9.4.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'boto' +version = '2.9.4' + +homepage = 'https://github.com/boto/boto/' +description = """Boto is a Python package that provides interfaces to Amazon Web Services.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/boto'], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb similarity index 55% rename from easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb rename to easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb index f6f2a181c2..0435b19fa5 100644 --- a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.13.eb +++ b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb @@ -1,7 +1,7 @@ -easyblock = 'VersionIndependentPythonPackage' +easyblock = 'PythonPackage' name = 'ecdsa' -version = '0.13' +version = '0.11' homepage = 'http://github.com/warner/python-ecdsa' description = """ECDSA cryptographic signature library (pure Python).""" @@ -11,6 +11,12 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# install into a path that's no specific to the Python version being used +installopts = "--install-lib=%(installdir)s/lib --no-compile" + sanity_check_paths = { 'files': [], 'dirs': ['lib/ecdsa'], diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index cfeb39d2cd..a1b1ee32cd 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -7,20 +7,28 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + dependencies = [ - ('ecdsa', '0.13'), # required for paramiko + ('ecdsa', '0.11'), # required for paramiko ('pycrypto', '2.6.1'), # required for paramiko - ('paramiko', '1.15.2'), + ('paramiko', '1.13.0'), ('PrettyTable', '0.7.2'), - ('pyCLI', '20140329'), - ('SQLAlchemy', '1.0.5'), - ('parsedatetime', '1.4'), + ('pyCLI', '2.0.3'), + ('SQLAlchemy', '0.7.9'), + ('parsedatetime', '0.8.7'), + ('boto', '2.9.4'), + ('python-novaclient', '2.15.0'), ] +# make sure a sufficiently recent setuptools is used, to avoid 'DistributionNotFound' errors +# see also http://www.fabfile.org/faq.html +builddependencies = [('setuptools', '17.1.1')] options = {'modulename': 'gc3libs'} @@ -29,4 +37,6 @@ sanity_check_paths = { 'dirs': ['lib/gc3utils', 'lib/gc3libs'] } +sanity_check_commands = [('gc3utils', 'info --version')] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb b/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb new file mode 100644 index 0000000000..42dfb305fb --- /dev/null +++ b/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'iso8601' +version = '0.1.10' + +homepage = 'https://bitbucket.org/micktwomey/pyiso8601/' +description = """Simple module to parse ISO 8601 dates""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/iso8601'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb b/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb similarity index 79% rename from easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb rename to easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb index fb4a02667b..ba205dd760 100644 --- a/easybuild/easyconfigs/p/paramiko/paramiko-1.15.2.eb +++ b/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb @@ -1,18 +1,18 @@ easyblock = 'VersionIndependentPythonPackage' name = 'paramiko' -version = '1.15.2' +version = '1.13.0' homepage = 'https://github.com/paramiko/paramiko/' description = """Native Python SSHv2 protocol library""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ - ('ecdsa', '0.13'), + ('ecdsa', '0.11'), ('pycrypto', '2.6.1'), ] diff --git a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb similarity index 95% rename from easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb rename to easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb index 181df165c0..6575af2226 100644 --- a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-1.4.eb +++ b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb @@ -1,7 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' name = 'parsedatetime' -version = '1.4' +version = '0.8.7' homepage = 'http://github.com/bear/parsedatetime/' description = """Parse human-readable date/time text.""" diff --git a/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb b/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb new file mode 100644 index 0000000000..2d32a2ff46 --- /dev/null +++ b/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb @@ -0,0 +1,21 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'pbr' +version = '0.5.21' + +homepage = 'https://launchpad.net/pbr' +description = """PBR is a library that injects some useful and sensible default behaviors into your setuptools run.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('pip', '7.0.3')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/pbr'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pip/pip-7.0.3.eb b/easybuild/easyconfigs/p/pip/pip-7.0.3.eb new file mode 100644 index 0000000000..edb2a34b6f --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-7.0.3.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'pip' +version = '7.0.3' + +homepage = 'https://pip.pypa.io/' +description = """he PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/pip'], + 'dirs': ['lib/pip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb b/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb similarity index 78% rename from easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb rename to easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb index 8c1d8067dd..4d71b105aa 100644 --- a/easybuild/easyconfigs/p/pyCLI/pyCLI-20140329.eb +++ b/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb @@ -1,7 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' name = 'pyCLI' -version = '20140329' +version = '2.0.3' homepage = 'http://packages.python.org/pyCLI/' description = """Simple, object-oriented approach to Python CLI apps""" @@ -9,8 +9,7 @@ description = """Simple, object-oriented approach to Python CLI apps""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [PYPI_SOURCE] -sources = ['pyCLI-devel.tar.gz'] -checksums = ['5cad880168f3423a1235b396735c1360'] +sources = [SOURCE_TAR_GZ] options = {'modulename': 'cli'} diff --git a/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb b/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb new file mode 100644 index 0000000000..28c6db9637 --- /dev/null +++ b/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb @@ -0,0 +1,32 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'python-novaclient' +version = '2.15.0' + +homepage = 'https://git.openstack.org/cgit/openstack/python-novaclient' +description = """Client library for OpenStack Compute API""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('pbr', '0.5.21'), + ('Babel', '1.3'), + ('PrettyTable', '0.7.2'), + ('simplejson', '3.7.3'), + ('requests', '2.4.2'), + ('iso8601', '0.1.10'), + ('argparse', '1.3.0'), + ('six', '1.9.0'), +] + +options = {'modulename': 'novaclient'} + +sanity_check_paths = { + 'files': ['bin/nova'], + 'dirs': ['lib/novaclient'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb b/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb new file mode 100644 index 0000000000..5bcf8c4fa0 --- /dev/null +++ b/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'pytz' +version = '2015.4' + +homepage = 'http://pythonhosted.org/pytz' +description = """World timezone definitions, modern and historical""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/pytz'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/requests/requests-2.4.2.eb b/easybuild/easyconfigs/r/requests/requests-2.4.2.eb new file mode 100644 index 0000000000..c3bc39cdc8 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.4.2.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'requests' +version = '2.4.2' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/requests'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb similarity index 95% rename from easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb rename to easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb index 2354094058..8483b950e9 100644 --- a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-1.0.5.eb +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' name = 'SQLAlchemy' -version = '1.0.5' +version = '0.7.9' homepage = 'http://www.sqlalchemy.org/' description = """Database Abstraction Library - The Python SQL Toolkit and Object Relational Mapper""" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb b/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb new file mode 100644 index 0000000000..29af11dc0f --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'setuptools' +version = '17.1.1' + +homepage = 'https://pypi.python.org/pypi/setuptools/' +description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/easy_install'], + 'dirs': ['lib/setuptools'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb b/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb new file mode 100644 index 0000000000..c88c56893e --- /dev/null +++ b/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'simplejson' +version = '3.7.3' + +homepage = 'http://github.com/simplejson/simplejson' +description = """Simple, fast, extensible JSON encoder/decoder for Python.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/simplejson'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/six/six-1.9.0.eb b/easybuild/easyconfigs/s/six/six-1.9.0.eb new file mode 100644 index 0000000000..a91199175e --- /dev/null +++ b/easybuild/easyconfigs/s/six/six-1.9.0.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'six' +version = '1.9.0' + +homepage = 'http://pypi.python.org/pypi/six' +description = """Python 2 and 3 compatibility utilities""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/six.py'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 64c1bc883c738279450d399c8ae0349920a35731 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 13:41:53 +0200 Subject: [PATCH 732/992] install GC3Pie as a bundle of Python packages --- .../easyconfigs/a/argparse/argparse-1.3.0.eb | 19 ------- easybuild/easyconfigs/b/Babel/Babel-1.3.eb | 21 ------- easybuild/easyconfigs/b/boto/boto-2.9.4.eb | 19 ------- easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb | 25 --------- .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 55 ++++++++++++------- .../easyconfigs/i/iso8601/iso8601-0.1.10.eb | 19 ------- .../p/PrettyTable/PrettyTable-0.7.2.eb | 20 ------- .../easyconfigs/p/paramiko/paramiko-1.13.0.eb | 24 -------- .../p/parsedatetime/parsedatetime-0.8.7.eb | 19 ------- easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb | 21 ------- easybuild/easyconfigs/p/pip/pip-7.0.3.eb | 19 ------- easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb | 21 ------- .../easyconfigs/p/pycrypto/pycrypto-2.6.1.eb | 29 ---------- .../python-novaclient-2.15.0.eb | 32 ----------- easybuild/easyconfigs/p/pytz/pytz-2015.4.eb | 19 ------- .../easyconfigs/r/requests/requests-2.4.2.eb | 19 ------- .../s/SQLAlchemy/SQLAlchemy-0.7.9.eb | 19 ------- .../s/setuptools/setuptools-17.1.1.eb | 19 ------- .../s/simplejson/simplejson-3.7.3.eb | 19 ------- easybuild/easyconfigs/s/six/six-1.9.0.eb | 19 ------- 20 files changed, 36 insertions(+), 421 deletions(-) delete mode 100644 easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb delete mode 100644 easybuild/easyconfigs/b/Babel/Babel-1.3.eb delete mode 100644 easybuild/easyconfigs/b/boto/boto-2.9.4.eb delete mode 100644 easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb delete mode 100644 easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb delete mode 100644 easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb delete mode 100644 easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb delete mode 100644 easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb delete mode 100644 easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb delete mode 100644 easybuild/easyconfigs/p/pip/pip-7.0.3.eb delete mode 100644 easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb delete mode 100644 easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb delete mode 100644 easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb delete mode 100644 easybuild/easyconfigs/p/pytz/pytz-2015.4.eb delete mode 100644 easybuild/easyconfigs/r/requests/requests-2.4.2.eb delete mode 100644 easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb delete mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb delete mode 100644 easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb delete mode 100644 easybuild/easyconfigs/s/six/six-1.9.0.eb diff --git a/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb b/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb deleted file mode 100644 index 6200884242..0000000000 --- a/easybuild/easyconfigs/a/argparse/argparse-1.3.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'argparse' -version = '1.3.0' - -homepage = 'http://code.google.com/p/argparse/' -description = """Python command-line parsing library""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['lib/argparse.py'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Babel/Babel-1.3.eb b/easybuild/easyconfigs/b/Babel/Babel-1.3.eb deleted file mode 100644 index 916af760ce..0000000000 --- a/easybuild/easyconfigs/b/Babel/Babel-1.3.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'Babel' -version = '1.3' - -homepage = 'http://babel.pocoo.org/' -description = """A collection of tools for internationalizing Python applications.""" - -toolchain = {'name': 'dummy', 'version': ''} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [('pytz', '2015.4')] - -sanity_check_paths = { - 'files': ['bin/pybabel'], - 'dirs': ['lib/babel'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/boto/boto-2.9.4.eb b/easybuild/easyconfigs/b/boto/boto-2.9.4.eb deleted file mode 100644 index bec02fba24..0000000000 --- a/easybuild/easyconfigs/b/boto/boto-2.9.4.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'boto' -version = '2.9.4' - -homepage = 'https://github.com/boto/boto/' -description = """Boto is a Python package that provides interfaces to Amazon Web Services.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['lib/boto'], - 'dirs': ['bin'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb b/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb deleted file mode 100644 index 0435b19fa5..0000000000 --- a/easybuild/easyconfigs/e/ecdsa/ecdsa-0.11.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'ecdsa' -version = '0.11' - -homepage = 'http://github.com/warner/python-ecdsa' -description = """ECDSA cryptographic signature library (pure Python).""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -# allow use of system Python -allow_system_deps = [('Python', SYS_PYTHON_VERSION)] - -# install into a path that's no specific to the Python version being used -installopts = "--install-lib=%(installdir)s/lib --no-compile" - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/ecdsa'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index a1b1ee32cd..900ad6b418 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -1,4 +1,4 @@ -easyblock = 'VersionIndependentPythonPackage' +easyblock = 'Bundle' name = 'GC3Pie' version = '2.2.3' @@ -7,34 +7,51 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] -dependencies = [ - ('ecdsa', '0.11'), # required for paramiko - ('pycrypto', '2.6.1'), # required for paramiko - ('paramiko', '1.13.0'), - ('PrettyTable', '0.7.2'), - ('pyCLI', '2.0.3'), - ('SQLAlchemy', '0.7.9'), - ('parsedatetime', '0.8.7'), - ('boto', '2.9.4'), - ('python-novaclient', '2.15.0'), +ext_options = { + 'source_urls': [PYPI_LOWER_SOURCE], + 'source_tmpl': '%(name)s-%(version)s.tar.gz', +} + +exts_list = [ + ('setuptools', '17.1.1', ext_options), + ('ecdsa', '0.11', ext_options), # required for paramiko + ('pycrypto', '2.6.1', dict(ext_options.items() + [('modulename', 'Crypto')])), # required for paramiko + ('paramiko', '1.13.0', ext_options), + ('PrettyTable', '0.7.2', dict(ext_options.items() + [('source_tmpl', 'prettytable-%(version)s.tar.gz')])), + ('pyCLI', '2.0.3', dict(ext_options.items() + [('modulename', 'cli')])), + ('SQLAlchemy', '0.7.9', ext_options), + ('parsedatetime', '0.8.7', ext_options), + ('boto', '2.9.4', ext_options), + ('pip', '7.0.3'), # required for pbr + ('pbr', '0.11.0'), # required for python-novaclient + ('Babel', '1.3'), # required for python-novaclient + ('simplejson', '3.7.3'), # required for python-novaclient + ('requests', '2.4.2'), # required for python-novaclient + ('iso8601', '0.1.10'), # required for python-novaclient + ('argparse', '1.3.0'), # required for python-novaclient + ('six', '1.9.0'), # required for python-novaclient + ('python-novaclient', '2.15.0', dict(ext_options.items() + [('modulename', 'novaclient')])), + (name.lower(), version, dict(ext_options.items() + [('modulename', 'gc3libs')])), ] -# make sure a sufficiently recent setuptools is used, to avoid 'DistributionNotFound' errors -# see also http://www.fabfile.org/faq.html -builddependencies = [('setuptools', '17.1.1')] -options = {'modulename': 'gc3libs'} +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} + +full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': ['lib/gc3utils', 'lib/gc3libs'] + 'dirs': ['lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg/gc3libs' % {'pyver': pyshortver}], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb b/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb deleted file mode 100644 index 42dfb305fb..0000000000 --- a/easybuild/easyconfigs/i/iso8601/iso8601-0.1.10.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'iso8601' -version = '0.1.10' - -homepage = 'https://bitbucket.org/micktwomey/pyiso8601/' -description = """Simple module to parse ISO 8601 dates""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/iso8601'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb b/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb deleted file mode 100644 index a75ea18716..0000000000 --- a/easybuild/easyconfigs/p/PrettyTable/PrettyTable-0.7.2.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'PrettyTable' -version = '0.7.2' - -homepage = 'http://code.google.com/p/prettytable/' -description = """PrettyTable is a simple Python library designed to make it quick and easy to represent tabular data - in visually appealing ASCII tables.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['lib/prettytable.py'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb b/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb deleted file mode 100644 index ba205dd760..0000000000 --- a/easybuild/easyconfigs/p/paramiko/paramiko-1.13.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'paramiko' -version = '1.13.0' - -homepage = 'https://github.com/paramiko/paramiko/' -description = """Native Python SSHv2 protocol library""" - -toolchain = {'name': 'dummy', 'version': ''} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('ecdsa', '0.11'), - ('pycrypto', '2.6.1'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/paramiko'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb b/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb deleted file mode 100644 index 6575af2226..0000000000 --- a/easybuild/easyconfigs/p/parsedatetime/parsedatetime-0.8.7.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'parsedatetime' -version = '0.8.7' - -homepage = 'http://github.com/bear/parsedatetime/' -description = """Parse human-readable date/time text.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/parsedatetime'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb b/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb deleted file mode 100644 index 2d32a2ff46..0000000000 --- a/easybuild/easyconfigs/p/pbr/pbr-0.5.21.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'pbr' -version = '0.5.21' - -homepage = 'https://launchpad.net/pbr' -description = """PBR is a library that injects some useful and sensible default behaviors into your setuptools run.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [('pip', '7.0.3')] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/pbr'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pip/pip-7.0.3.eb b/easybuild/easyconfigs/p/pip/pip-7.0.3.eb deleted file mode 100644 index edb2a34b6f..0000000000 --- a/easybuild/easyconfigs/p/pip/pip-7.0.3.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'pip' -version = '7.0.3' - -homepage = 'https://pip.pypa.io/' -description = """he PyPA recommended tool for installing Python packages.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['bin/pip'], - 'dirs': ['lib/pip'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb b/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb deleted file mode 100644 index 4d71b105aa..0000000000 --- a/easybuild/easyconfigs/p/pyCLI/pyCLI-2.0.3.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'pyCLI' -version = '2.0.3' - -homepage = 'http://packages.python.org/pyCLI/' -description = """Simple, object-oriented approach to Python CLI apps""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -options = {'modulename': 'cli'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/cli'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb b/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb deleted file mode 100644 index 88292f1478..0000000000 --- a/easybuild/easyconfigs/p/pycrypto/pycrypto-2.6.1.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pycrypto' -version = '2.6.1' - -homepage = 'http://www.pycrypto.org/' -description = """Cryptographic modules for Python.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -# allow use of system Python -allow_system_deps = [('Python', SYS_PYTHON_VERSION)] - -# install into a path that's no specific to the Python version being used -installopts = '--install-lib=%(installdir)s/lib --no-compile' - -options = {'modulename': 'Crypto'} - -modextrapaths = {'PYTHONPATH': ['lib']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/Crypto'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb b/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb deleted file mode 100644 index 28c6db9637..0000000000 --- a/easybuild/easyconfigs/p/python-novaclient/python-novaclient-2.15.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'python-novaclient' -version = '2.15.0' - -homepage = 'https://git.openstack.org/cgit/openstack/python-novaclient' -description = """Client library for OpenStack Compute API""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('pbr', '0.5.21'), - ('Babel', '1.3'), - ('PrettyTable', '0.7.2'), - ('simplejson', '3.7.3'), - ('requests', '2.4.2'), - ('iso8601', '0.1.10'), - ('argparse', '1.3.0'), - ('six', '1.9.0'), -] - -options = {'modulename': 'novaclient'} - -sanity_check_paths = { - 'files': ['bin/nova'], - 'dirs': ['lib/novaclient'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb b/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb deleted file mode 100644 index 5bcf8c4fa0..0000000000 --- a/easybuild/easyconfigs/p/pytz/pytz-2015.4.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'pytz' -version = '2015.4' - -homepage = 'http://pythonhosted.org/pytz' -description = """World timezone definitions, modern and historical""" - -toolchain = {'name': 'dummy', 'version': ''} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/pytz'] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/requests/requests-2.4.2.eb b/easybuild/easyconfigs/r/requests/requests-2.4.2.eb deleted file mode 100644 index c3bc39cdc8..0000000000 --- a/easybuild/easyconfigs/r/requests/requests-2.4.2.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'requests' -version = '2.4.2' - -homepage = 'https://pypi.python.org/pypi/requests' -description = """Python http for humans""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/requests'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb deleted file mode 100644 index 8483b950e9..0000000000 --- a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-0.7.9.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'SQLAlchemy' -version = '0.7.9' - -homepage = 'http://www.sqlalchemy.org/' -description = """Database Abstraction Library - The Python SQL Toolkit and Object Relational Mapper""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/sqlalchemy'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb b/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb deleted file mode 100644 index 29af11dc0f..0000000000 --- a/easybuild/easyconfigs/s/setuptools/setuptools-17.1.1.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'setuptools' -version = '17.1.1' - -homepage = 'https://pypi.python.org/pypi/setuptools/' -description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['bin/easy_install'], - 'dirs': ['lib/setuptools'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb b/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb deleted file mode 100644 index c88c56893e..0000000000 --- a/easybuild/easyconfigs/s/simplejson/simplejson-3.7.3.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'simplejson' -version = '3.7.3' - -homepage = 'http://github.com/simplejson/simplejson' -description = """Simple, fast, extensible JSON encoder/decoder for Python.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/simplejson'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/six/six-1.9.0.eb b/easybuild/easyconfigs/s/six/six-1.9.0.eb deleted file mode 100644 index a91199175e..0000000000 --- a/easybuild/easyconfigs/s/six/six-1.9.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'VersionIndependentPythonPackage' - -name = 'six' -version = '1.9.0' - -homepage = 'http://pypi.python.org/pypi/six' -description = """Python 2 and 3 compatibility utilities""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -sanity_check_paths = { - 'files': ['lib/six.py'], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From d3d531982170ea29b4d5cc5dbd643074f990e2c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 14:06:46 +0200 Subject: [PATCH 733/992] fix source_urls for GC3Pie easyconfig --- .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 96 ++++++++++++++----- 1 file changed, 72 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index 900ad6b418..e3154cc1a9 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -16,31 +16,79 @@ exts_filter = ('python -c"import %(ext_name)s"', '') # allow use of system Python allow_system_deps = [('Python', SYS_PYTHON_VERSION)] -ext_options = { - 'source_urls': [PYPI_LOWER_SOURCE], - 'source_tmpl': '%(name)s-%(version)s.tar.gz', -} - exts_list = [ - ('setuptools', '17.1.1', ext_options), - ('ecdsa', '0.11', ext_options), # required for paramiko - ('pycrypto', '2.6.1', dict(ext_options.items() + [('modulename', 'Crypto')])), # required for paramiko - ('paramiko', '1.13.0', ext_options), - ('PrettyTable', '0.7.2', dict(ext_options.items() + [('source_tmpl', 'prettytable-%(version)s.tar.gz')])), - ('pyCLI', '2.0.3', dict(ext_options.items() + [('modulename', 'cli')])), - ('SQLAlchemy', '0.7.9', ext_options), - ('parsedatetime', '0.8.7', ext_options), - ('boto', '2.9.4', ext_options), - ('pip', '7.0.3'), # required for pbr - ('pbr', '0.11.0'), # required for python-novaclient - ('Babel', '1.3'), # required for python-novaclient - ('simplejson', '3.7.3'), # required for python-novaclient - ('requests', '2.4.2'), # required for python-novaclient - ('iso8601', '0.1.10'), # required for python-novaclient - ('argparse', '1.3.0'), # required for python-novaclient - ('six', '1.9.0'), # required for python-novaclient - ('python-novaclient', '2.15.0', dict(ext_options.items() + [('modulename', 'novaclient')])), - (name.lower(), version, dict(ext_options.items() + [('modulename', 'gc3libs')])), + ('setuptools', '17.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '0.7.9', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '0.8.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.9.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '0.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.15.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), ] pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) -- GitLab From f62823897b177a93a09d8b194df90b08063f2b32 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 16:12:30 +0200 Subject: [PATCH 734/992] include both lib and lib64 in $PYTHONPATH in GC3Pie easyconfig --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index e3154cc1a9..d8254ca575 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -93,7 +93,8 @@ exts_list = [ pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) -modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver]} +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver]} full_sanity_check = True -- GitLab From a26edced5925bc4ea05e4c7fe363c432d1989200 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 16:27:28 +0200 Subject: [PATCH 735/992] fix source_urls for argparse Python extension --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 2 +- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb | 2 +- 47 files changed, 47 insertions(+), 47 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 08ae2a5f52..aa976378fe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -59,7 +59,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 5691adf05e..1977d33177 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -59,7 +59,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 8bf00ee94a..b82404eb26 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index 2ade7ad4f1..0eaf32ef4a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index a73fef035d..aeb1a5dbe8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index 2af2f0c181..5708c09083 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index 0218dcafbd..d0197126f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 342b19c101..2c3b844cef 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index b883b3a7a7..d2fb8dbf98 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index 53fb8ff292..8af79fb950 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index c2cc52183e..4715f5d29d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 994f20889f..9e8e258f1e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 459199e8c5..4ea3681947 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index 3e4b4f03f3..055d5c5563 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 2e8be6d925..8e32b0f084 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index c6d6010f0e..77656f8d16 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 2da448273b..ad5369bd07 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index b7849aec58..bbc8eab1c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index c17df2cb09..6186a3614b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index 9f5cd7d95f..e943c91436 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index a24d0b3e6e..b2b682da04 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index cee2b8e189..09ce3003e9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index 751a483994..ea85f15f15 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -52,7 +52,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 8b46b16cd3..c14fdff5ce 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -52,7 +52,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index ed13d94285..23aec43a01 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -56,7 +56,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 8e7a62f6da..42b742d915 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index aaba09ba09..3cc492d6b4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index d9f7ad0b77..0c53db7e43 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 6e042b928d..31ea2a894b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 09dc45c1e6..5c19bcd953 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -60,7 +60,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 383b7d978b..f1ec579fbe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -61,7 +61,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index 18aa12a4b8..b620899273 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 787f5ecab1..1ae3ec0c5f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index 16a9eea25f..60923e701c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index 39d6b11c34..2e085966c7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index 466ad2cc0c..0c1b139dda 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index 5a66cda69a..186e5f94df 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index d0661c356d..e5b95d6f14 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index cc0e90d0e3..bb297e5eb8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index bb0fac1650..27281d943c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index ed4d77fc45..2c04d1e9a7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index 033d183105..66a6b2687c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index c928dc3ca3..ce554428cd 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index f523509a1d..3e3d09b0be 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index a47ee809f5..98228f8b19 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index d3f83f3c59..b7690d84fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -61,7 +61,7 @@ exts_list = [ ], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 9f71e6e86f..91935078a9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -61,7 +61,7 @@ exts_list = [ ], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], -- GitLab From 7bc30033e5b9c5015c0c8a2e96912b8fb99ab18d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jun 2015 17:35:47 +0200 Subject: [PATCH 736/992] fix source_urls for deap Python extension --- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 2 +- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- 31 files changed, 31 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index b82404eb26..b447f3f5c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index 0eaf32ef4a..3b9b9b0071 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index aeb1a5dbe8..e9411a98a0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index 5708c09083..9d81cee86b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index d0197126f1..b7dfb64df9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 2c3b844cef..5eb4c88938 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index d2fb8dbf98..878951cc6e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index 8af79fb950..957d719fbd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 4715f5d29d..49da1ce96f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 9e8e258f1e..ff029a2234 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 4ea3681947..2ef8f9fc88 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index 055d5c5563..b5075a6a9a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 8e32b0f084..e1bc68f6d1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 77656f8d16..1f6678ca73 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index ad5369bd07..bcc80770f8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index bbc8eab1c5..262801c6c1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 6186a3614b..7713f86879 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -71,7 +71,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index e943c91436..0acac864f5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index b2b682da04..b8e12d524c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index 09ce3003e9..9fda7777e6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index ea85f15f15..6f7edf431e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -68,7 +68,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index c14fdff5ce..3c2a47e51e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -68,7 +68,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index 23aec43a01..c8797b36e9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -72,7 +72,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 42b742d915..de11eaf356 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index 3cc492d6b4..b8f2f71c12 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 0c53db7e43..be1053a62d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 31ea2a894b..caf05b2cc7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index 66a6b2687c..ddf1d2d853 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index ce554428cd..86066e4a5e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index 3e3d09b0be..b01168b83e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 98228f8b19..de9617eacf 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], -- GitLab From 71581ecabb33f908cf4e6f1b50bdc5d3f1e65ac8 Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 16 Jun 2015 14:49:30 +0200 Subject: [PATCH 737/992] .eb file for Bowtie2-2.2.5-goolf-1.7.20 --- .../b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb new file mode 100644 index 0000000000..30dfc18960 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.5' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' -- GitLab From 46d48a8687599e68e33e1ec5f9b06cab652a3a60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Jun 2015 15:12:00 +0200 Subject: [PATCH 738/992] {vis}[*/2015a] Pillow 2.8.1 --- .../Pillow-2.8.1-foss-2015a-Python-2.7.9.eb | 23 +++++++++++++++++++ .../Pillow-2.8.1-intel-2015a-Python-2.7.9.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..524dd9ba3d --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.8.1' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..04c7f0efa3 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.8.1' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' -- GitLab From 9eb0080c3f24d806d39f0ddf887797bebd53107a Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 16 Jun 2015 17:56:59 +0200 Subject: [PATCH 739/992] .eb file for Python-2.7.9-goolf-1.7.20 --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 119 ++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb new file mode 100644 index 0000000000..324a98e966 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -0,0 +1,119 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('SQLite', '3.8.8.1'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('requests', '2.6.2', { + 'source_urls': ['http://pypi.python.org/packages/source/r/requests/'], + }), + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + + +moduleclass = 'lang' -- GitLab From 0327feff827d5a017ad8322f9e2e76bd6d51a07f Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 16 Jun 2015 18:17:26 +0200 Subject: [PATCH 740/992] .eb file for LibTIFF-4.0.3-goolf-1.7.20 --- .../l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb new file mode 100644 index 0000000000..46a3c3ee49 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.3' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 343db5ac56707f338adc6b7a1a0aef48ba2d2d93 Mon Sep 17 00:00:00 2001 From: npklein Date: Tue, 16 Jun 2015 20:20:27 +0200 Subject: [PATCH 741/992] .eb for libgtextutils-0.6.1-goolf-1.7.2 --- .../libgtextutils-0.6.1-goolf-1.7.20.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..89f72fe364 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'libgtextutils' +version = '0.6.1' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] + } + +moduleclass = 'bio' -- GitLab From b69ab3196178cebcada2c3387dc4ee9b9692d176 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 07:48:43 +0200 Subject: [PATCH 742/992] fix easyconfigs unit tests after making ModulesTool a non-singleton class (cfr. https://github.com/hpcugent/easybuild-framework/pull/1299) --- test/easyconfigs/easyconfigs.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 6efa3b178f..12d11afc1e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -32,6 +32,7 @@ import copy import glob import os import re +import shutil import sys import tempfile from distutils.version import LooseVersion @@ -48,6 +49,7 @@ from easybuild.framework.easyconfig.easyconfig import get_easyblock_class from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config +from easybuild.tools.filetools import write_file from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool @@ -79,10 +81,10 @@ class EasyConfigTest(TestCase): config.set_tmpdir() del eb_go - # mock 'exist' and 'load' methods of modules tool, which are used for 'craype' external module - modtool = modules_tool() - modtool.exist = lambda m: [True]*len(m) - modtool.load = lambda m: True + # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains + TMPDIR = tempfile.mkdtemp() + os.environ['MODULEPATH'] = TMPDIR + write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n') log = fancylogger.getLogger("EasyConfigTest", fname=False) @@ -227,6 +229,10 @@ class EasyConfigTest(TestCase): if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + def test_zzz_cleanup(self): + """Dummy test to clean up global temporary directory.""" + shutil.rmtree(self.TMPDIR) + def template_easyconfig_test(self, spec): """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" -- GitLab From 5da2cf5a61420352c9cb9ef290abdbd3c413a929 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 3 Jun 2015 13:15:57 +0200 Subject: [PATCH 743/992] Add support for R pbd. --- ...bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 45 +++++++++++++++++++ ..._ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb create mode 100644 easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb new file mode 100644 index 0000000000..05e79faaa5 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'R-bundle' +version = '20150605' +bundlename = 'pbd' +rver = '3.1.3' +versionsuffix = '-R-%s-%s' % (rver, bundlename) + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('pbdMPI', '0.2-5', ext_options), + ('pbdSLAP', '0.2-0', ext_options), + ('pbdBASE', '0.2-3', dict(ext_options.items() + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), + ('pbdDMAT', '0.2-3', ext_options), + ('pbdDEMO', '0.2-0', ext_options), + ('pmclust', '0.1-6', ext_options), + ('EMCluster', '0.2-4', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch new file mode 100644 index 0000000000..ae54615b78 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch @@ -0,0 +1,45 @@ +# Add support for intel mpi by removing references to BI_COMM_WORLD +# BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. +--- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 ++++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 +@@ -25,7 +25,9 @@ + BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; + BLACS_APTS.BI_MyContxts = BI_MyContxts; + BLACS_APTS.BI_SysContxts = BI_SysContxts; ++#ifndef __INTEL_COMPILER + BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; ++#endif + BLACS_APTS.BI_Stats = BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -44,7 +46,9 @@ + BI_AuxBuff.nAops, BI_AuxBuff.N); + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); ++#ifndef __INTEL_COMPILER + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#endif + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); +@@ -89,7 +93,9 @@ + + BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; + BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; ++#ifndef __INTEL_COMPILER + BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; ++#endif + BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -109,7 +115,9 @@ + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#ifndef __INTEL_COMPILER + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); ++#endif + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); + } + -- GitLab From e86709617e63f62a0de934294f6ebce461571c82 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 10:21:50 +0200 Subject: [PATCH 744/992] Use SOURCEFORGE_SOURCE as source urls, remove import time and seconds from epoch --- easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb | 5 +---- easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb | 5 +---- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb index 6278b4ba19..72296e698f 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb @@ -1,5 +1,3 @@ -import time - easyblock = 'PackedBinary' name = 'snpEff' @@ -17,8 +15,7 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -seconds_after_epoch = int(time.time()) -source_urls = [('http://downloads.sourceforge.net/project/%s?ts=%s&use_mirror=autoselect' % (name.lower(), seconds_after_epoch))] +source_urls = [SOURCEFORGE_SOURCE] sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] checksums = ['f4571413833df913261ff76b6f40bb76'] diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb index 7763b7baad..7e0c5d595f 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb @@ -1,5 +1,3 @@ -import time - easyblock = 'PackedBinary' name = 'snpEff' @@ -17,8 +15,7 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -seconds_after_epoch = int(time.time()) -source_urls = ['http://downloads.sourceforge.net/project/%(name.lower())s?ts=%(seconds_after_epoch)s&use_mirror=autoselect'] +source_urls = [SOURCEFORGE_SOURCE] sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] -- GitLab From a5f6037e278342781100925ffcfd1708806e9424 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 10:23:44 +0200 Subject: [PATCH 745/992] removed first empty line --- easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb index ceb5083895..cb7232a3fb 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb @@ -1,4 +1,3 @@ - name = 'SAMtools' version = '0.1.19' -- GitLab From 382c292d5f92e4f79336b446c5e2d579000101e8 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 10:48:00 +0200 Subject: [PATCH 746/992] Change v to in filename --- .../s/snpEff/snpEff-3.6-Java-1.7.0_80.eb | 28 +++++++++++++++++++ .../s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000..72296e698f --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '3.6' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. +It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +source_urls = [SOURCEFORGE_SOURCE] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +checksums = ['f4571413833df913261ff76b6f40bb76'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb new file mode 100644 index 0000000000..7e0c5d595f --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '4.1d' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. +It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +source_urls = [SOURCEFORGE_SOURCE] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From a7b9d66efdc3eca679266dc6c772fce3db0ac74f Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 11:06:40 +0200 Subject: [PATCH 747/992] remove snpEff files with wrong file name --- .../s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb | 28 ------------------- .../s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb | 28 ------------------- 2 files changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb delete mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb deleted file mode 100644 index 72296e698f..0000000000 --- a/easybuild/easyconfigs/s/snpEff/snpEff-v3.6-Java-1.7.0_80.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'snpEff' -version = '3.6' - -homepage = 'http://sourceforge.net/projects/snpeff/' -description = """SnpEff is a variant annotation and effect prediction tool. -It annotates and predicts the effects of genetic variants (such as amino acid changes).""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] - -source_urls = [SOURCEFORGE_SOURCE] -sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] - -checksums = ['f4571413833df913261ff76b6f40bb76'] - -sanity_check_paths = { - 'files': ['snpEff.jar', 'SnpSift.jar'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb deleted file mode 100644 index 7e0c5d595f..0000000000 --- a/easybuild/easyconfigs/s/snpEff/snpEff-v4.1d-Java-1.7.0_80.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'snpEff' -version = '4.1d' - -homepage = 'http://sourceforge.net/projects/snpeff/' -description = """SnpEff is a variant annotation and effect prediction tool. -It annotates and predicts the effects of genetic variants (such as amino acid changes).""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -java = 'Java' -javaver = '1.7.0_80' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] - -source_urls = [SOURCEFORGE_SOURCE] -sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] - -checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] - -sanity_check_paths = { - 'files': ['snpEff.jar', 'SnpSift.jar'], - 'dirs': [] -} - -moduleclass = 'bio' -- GitLab From b60a9309274819261ed452d19547dad4dbe1d372 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 12:01:04 +0200 Subject: [PATCH 748/992] Change http to https --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index 324a98e966..a97b98d87d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -1,7 +1,7 @@ name = 'Python' version = '2.7.9' -homepage = 'http://python.org/' +homepage = 'https://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." toolchain = {'name': 'goolf', 'version': '1.7.20'} @@ -10,7 +10,7 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} numpyversion = '1.9.1' scipyversion = '0.14.1' -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package @@ -30,34 +30,34 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('requests', '2.6.2', { - 'source_urls': ['http://pypi.python.org/packages/source/r/requests/'], + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], }), ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'source_urls': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], }), ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + 'source_urls': [('https://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://argparse.googlecode.com/files/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -66,14 +66,14 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://www.cython.org/release/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], -- GitLab From 5287f6181d6772f1c1819828b44363e40721c332 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 12:01:41 +0200 Subject: [PATCH 749/992] fix remark --- .../easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb | 1 + .../easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb | 32 +++++++++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index d8254ca575..8bb06bd90a 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -96,6 +96,7 @@ pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) # on RHEL-based systems, some extensions get installed to lib, some to lib64 modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver]} +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb new file mode 100644 index 0000000000..00e503af1d --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'GC3Pie' +version = '2.3.dev' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# svn checkout http://gc3pie.googlecode.com/svn/trunk/ gc3pie +# gc3pie-2.3.dev.tar.gz gc3pie +sources = ['gc3pie-%(version)s.tar.gz'] + +start_dir = 'gc3pie' + +# allow use of system python +allow_system_deps = [('python', SYS_PYTHON_VERSION)] + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +options = {'modulename': 'gc3libs'} + +sanity_check_paths = { + 'files': ['bin/gc3utils', 'lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg' % {'pyver': pyshortver}], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From b19f9deee3096685d3dfe64efc100be00608f6b7 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 12:12:51 +0200 Subject: [PATCH 750/992] fix indentation --- .../l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb index 89f72fe364..bf0770fd9f 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb @@ -24,8 +24,8 @@ sources = [SOURCE_TAR_BZ2] source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] sanity_check_paths = { - 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], - 'dirs': ['lib/pkgconfig'] - } + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] + } moduleclass = 'bio' -- GitLab From 2959ff50bbdf1d5a60aafedcea5419e590891c47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 12:17:37 +0200 Subject: [PATCH 751/992] remove easyconfig for GC3Pie dev version that crept in --- .../easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb deleted file mode 100644 index 00e503af1d..0000000000 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.dev.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'GC3Pie' -version = '2.3.dev' - -homepage = 'https://gc3pie.readthedocs.org' -description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution - environments.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# svn checkout http://gc3pie.googlecode.com/svn/trunk/ gc3pie -# gc3pie-2.3.dev.tar.gz gc3pie -sources = ['gc3pie-%(version)s.tar.gz'] - -start_dir = 'gc3pie' - -# allow use of system python -allow_system_deps = [('python', SYS_PYTHON_VERSION)] - -pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) - -options = {'modulename': 'gc3libs'} - -sanity_check_paths = { - 'files': ['bin/gc3utils', 'lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg' % {'pyver': pyshortver}], - 'dirs': [], -} - -sanity_check_commands = [('gc3utils', 'info --version')] - -moduleclass = 'tools' -- GitLab From 3ede896bf3f92cb21ea29b711bbde0c1cb613895 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 12:18:54 +0200 Subject: [PATCH 752/992] Change dependencies to include SQLite and OpenSSL and remove requests --- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index a97b98d87d..b70766f54b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -19,8 +19,8 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('SQLite', '3.8.8.1'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + ('SQLite', '3.8.8.1'), + ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] @@ -29,9 +29,6 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated Jan 19th 2015 exts_list = [ - ('requests', '2.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), ('setuptools', '11.3.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), -- GitLab From c7ea46925714e7124d9f72285eec965faa1c65c4 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:33:39 +0200 Subject: [PATCH 753/992] .eb file for freetype-2.5.3-goolf-1.7.20 --- .../f/freetype/freetype-2.5.3-goolf-1.7.20 | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 new file mode 100644 index 0000000000..c5fb92d43c --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.3' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.12')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' -- GitLab From 3aa0e15b4991d912c3677cf371853581abd076ec Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:35:26 +0200 Subject: [PATCH 754/992] remove Python-2.7.9-goolf-1.7.20.eb should be in Python branch --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 119 ------------------ 1 file changed, 119 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb deleted file mode 100644 index 324a98e966..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ /dev/null @@ -1,119 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('SQLite', '3.8.8.1'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('requests', '2.6.2', { - 'source_urls': ['http://pypi.python.org/packages/source/r/requests/'], - }), - ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], - }), - ('pbr', '0.10.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('mock', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2014.10', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], - }), -] - - -moduleclass = 'lang' -- GitLab From 350e1cd24f06f950b485e858e01aa86207116a47 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:37:50 +0200 Subject: [PATCH 755/992] .eb file for fontconfig-2.11.1-goolf-1.7.20 --- .../fontconfig/fontconfig-2.11.1-goolf-1.7.20 | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 new file mode 100644 index 0000000000..e77da2e1fe --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.5.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' -- GitLab From 5bf3948c1002e8da79db7570c71e4923ded83b00 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:38:38 +0200 Subject: [PATCH 756/992] remove Python-2.7.9-goolf-1.7.20.eb should be in Python branch --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 119 ------------------ 1 file changed, 119 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb deleted file mode 100644 index 324a98e966..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ /dev/null @@ -1,119 +0,0 @@ -name = 'Python' -version = '2.7.9' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.9.1' -scipyversion = '0.14.1' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('SQLite', '3.8.8.1'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# order is important! -# package versions updated Jan 19th 2015 -exts_list = [ - ('requests', '2.6.2', { - 'source_urls': ['http://pypi.python.org/packages/source/r/requests/'], - }), - ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], - }), - ('pbr', '0.10.8', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.10.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.21.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('six', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.4.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('paramiko', '1.15.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.13', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('mock', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2014.10', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], - }), -] - - -moduleclass = 'lang' -- GitLab From 30c2d6d35b0d54b4c932db203b14d885178e883c Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:42:28 +0200 Subject: [PATCH 757/992] .eb file for GLib-2.40.0-goolf-1.7.20 --- .../g/GLib/GLib-2.40.0-goolf-1.7.20.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..8949f8ac3a --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.40.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.1'), + ('gettext', '0.19.2'), +] +builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' -- GitLab From f93360c72fd77663ebe0ee8013b5017601a33eee Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:47:37 +0200 Subject: [PATCH 758/992] .eb file for libjpeg-turbo-1.3.1-goolf-1.7.20 --- .../libjpeg-turbo-1.3.1-goolf-1.7.20.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..d2b54d01ff --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.3.1' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' -- GitLab From eaed5bdeb7560fee2512f81dcdf392af636ee352 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:49:45 +0200 Subject: [PATCH 759/992] .eb file for libpng-1.6.12-goolf-1.7.20 --- .../l/libpng/libpng-1.6.12-goolf-1.7.20.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb new file mode 100644 index 0000000000..11dd528148 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.12' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' -- GitLab From db1282d0ea7f4feddc302d76930ec0ec3ab07494 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:52:18 +0200 Subject: [PATCH 760/992] .eb file for expat-2.1.0-goolf-1.7.20 --- .../e/expat/expat-2.1.0-goolf-1.7.20.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..721806cde9 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application +registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' -- GitLab From 599c5fd5a3b3c02e07eda23489d9cf3f04bdd479 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 12:54:26 +0200 Subject: [PATCH 761/992] .eb file for cairo-1.12.18-goolf-1.7.20 --- .../c/cairo/cairo-1.12.18-goolf-1.7.20.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb new file mode 100644 index 0000000000..e57987a01a --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.12.18' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. +Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, +PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('libpng', '1.6.12'), + ('freetype', '2.5.3'), + ('zlib', '1.2.8'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('expat', '2.1.0'), + ('bzip2', '1.0.6'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' -- GitLab From abed07bf25b3ed1216f0e985e9bb3d3dc0a07a88 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 13:31:32 +0200 Subject: [PATCH 762/992] The demo package is updated every 2-3 months, i.e., a checksum doesn't make much sense --- .../easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb index 42c77ab311..4151c18955 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb @@ -27,10 +27,6 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] -checksums = [ - '09cf28650be36516613372c8a0d1c0d8', # vampir-8.4.1-demo-linux-x86_64-setup.bin -] - install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { -- GitLab From 8acb4772bfc7299afe940f911afc253c162e080c Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 13:36:37 +0200 Subject: [PATCH 763/992] Don't use ALL_CAPS: VAMPIR -> Vampir --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb | 2 +- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb | 2 +- .../easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb index 4151c18955..e474d1fc46 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb @@ -18,7 +18,7 @@ versionsuffix = "-demo" variant = "linux-x86_64" homepage = 'http://www.vampir.eu' -description = """The VAMPIR software tool provides an easy-to-use framework that enables +description = """The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb index ffb4fc26ad..cdf8d18bde 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb @@ -17,7 +17,7 @@ version = "8.4.1" variant = "linux-x86_64" homepage = 'http://www.vampir.eu' -description = """The VAMPIR software tool provides an easy-to-use framework that enables +description = """The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb index 83d53b0104..29d61b1985 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb @@ -17,7 +17,7 @@ version = "8.4.1" variant = "linux-x86_64" homepage = 'http://www.vampir.eu' -description = """The VAMPIR software tool provides an easy-to-use framework that enables +description = """The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -- GitLab From 4a625e3c6f38f759c328a87bdb24ed1feae1e4ab Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 14:03:49 +0200 Subject: [PATCH 764/992] add blank line, left align } --- .../l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb index bf0770fd9f..b5f853d5af 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb @@ -17,6 +17,7 @@ version = '0.6.1' homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'pic': True} @@ -26,6 +27,6 @@ source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] sanity_check_paths = { 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], 'dirs': ['lib/pkgconfig'] - } +} moduleclass = 'bio' -- GitLab From 5ab1597eda0f040aa4373a00c821d64a575d80f1 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:14:18 +0200 Subject: [PATCH 765/992] add cairo dependency pixman 0.32.6-goolf-1.7.20 --- .../p/pixman/pixman-0.32.6-goolf-1.7.20.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb new file mode 100644 index 0000000000..9a915bad5f --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.32.6' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 227baad9b58bb155262a1e8fde9878c1c0307c7a Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:16:11 +0200 Subject: [PATCH 766/992] add .eb to fontconfig-2.11.1-goolf-1.7.20 --- .../fontconfig-2.11.1-goolf-1.7.20.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..e77da2e1fe --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.5.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' -- GitLab From 746c409b9aa762b589b1127f235ec9f378569977 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:17:34 +0200 Subject: [PATCH 767/992] remove fontconfig-2.11.1-goolf-1.7.20 --- .../fontconfig/fontconfig-2.11.1-goolf-1.7.20 | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 deleted file mode 100644 index e77da2e1fe..0000000000 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20 +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = "fontconfig" -version = '2.11.1' - -homepage = 'http://www.freedesktop.org/software/fontconfig' -description = """Fontconfig is a library designed to provide system-wide font configuration, customization and -application access.""" - -toolchain = {'name': 'goolf', 'version': '1.7.20'} - -source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('expat', '2.1.0'), - ('freetype','2.5.3'), -] - -configopts = '--disable-docs ' - -moduleclass = 'vis' -- GitLab From 38a40b4be0f4f7f3ba8c6cd231365a3eb7e908f1 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:32:18 +0200 Subject: [PATCH 768/992] Add dependency NASM-2.11.05-goolf-1.7.20.eb --- .../n/NASM/NASM-2.11.05-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb new file mode 100644 index 0000000000..61250ef0ab --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.05' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 8ca3279b83d5e25abc8451cdd1150ce552036c8e Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:35:08 +0200 Subject: [PATCH 769/992] add .eb after file --- ...freetype-2.5.3-goolf-1.7.20 => freetype-2.5.3-goolf-1.7.20.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/freetype/{freetype-2.5.3-goolf-1.7.20 => freetype-2.5.3-goolf-1.7.20.eb} (100%) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb similarity index 100% rename from easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20 rename to easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb -- GitLab From af6a2df0801cd6a584db168354831ca22b1fd34b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 14:39:15 +0200 Subject: [PATCH 770/992] Use minimal toolchains --- .../{Vampir-8.4.1-demo-foss-2015a.eb => Vampir-8.4.1-demo.eb} | 2 +- .../v/Vampir/{Vampir-8.4.1-foss-2015a.eb => Vampir-8.4.1.eb} | 2 +- ...er-8.4.1-foss-2015a.eb => VampirServer-8.4.1-gompi-2015a.eb} | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-demo-foss-2015a.eb => Vampir-8.4.1-demo.eb} (96%) rename easybuild/easyconfigs/v/Vampir/{Vampir-8.4.1-foss-2015a.eb => Vampir-8.4.1.eb} (96%) rename easybuild/easyconfigs/v/VampirServer/{VampirServer-8.4.1-foss-2015a.eb => VampirServer-8.4.1-gompi-2015a.eb} (96%) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb similarity index 96% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb index e474d1fc46..62ddb26846 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -23,7 +23,7 @@ description = """The Vampir software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb similarity index 96% rename from easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb rename to easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb index cdf8d18bde..379ca0d9f4 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -22,7 +22,7 @@ description = """The Vampir software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['vampir-%s-%s-setup.bin' % (version, variant)] diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb similarity index 96% rename from easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb rename to easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb index 29d61b1985..b3fef1121f 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -22,7 +22,7 @@ description = """The Vampir software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'foss', 'version': '2015a'} +toolchain = {'name': 'gompi', 'version': '2015a'} toolchainopts = {"usempi": True} sources = ['vampirserver-%s-%s-setup.bin' % (version, variant)] -- GitLab From 360d993e07be8da6e836a20374acf372d2999c35 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 14:54:03 +0200 Subject: [PATCH 771/992] few changes from @boegel his comments --- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index b70766f54b..2eabb347c9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + #('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['https://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/ '], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -63,7 +63,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.21.2', { - 'source_urls': ['https://www.cython.org/release/'], + 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], -- GitLab From f591d8b70dac8679ba3b60ba2c9d84b71cad2616 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 14:57:15 +0200 Subject: [PATCH 772/992] add depedency SQLite-3.8.8.1-goolf-1.7.20.eb --- .../s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..ee10abf948 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 92e0aaa1cfae7791c39f4fa8a306e2814a608b00 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 15:03:06 +0200 Subject: [PATCH 773/992] fix remarks w.r.t. missing comments --- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 ++ easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 1 + .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 ++ easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 1 + .../easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 1 + .../easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb | 1 + 6 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index cb9289d4be..6b906969bb 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -12,7 +12,9 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] builddependencies = [ + # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 8aefcfeeee..3b30b6d478 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +# zlib required, but being linked instatically, so not a runtime dep builddependencies = [('zlib', '1.2.8')] # statically link with zlib, to avoid runtime dependency on zlib diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index fa4ce3cee9..e8d57cd578 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -12,7 +12,9 @@ sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] builddependencies = [ + # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 3c7395c4a9..aa312b1626 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +# zlib required, but being linked instatically, so not a runtime dep builddependencies = [('zlib', '1.2.8')] # statically link with zlib, to avoid runtime dependency on zlib diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb index 3f419579d9..71c0cc0f49 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +# use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb index d10f6ce0ce..797739b09a 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +# use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { -- GitLab From e6df0d70a70b150a71dd547594c0e451c8155c43 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 15:17:50 +0200 Subject: [PATCH 774/992] fix Xmipp easyconfigs: naming, patches, deps + add foss/2015a equivalent --- .../Xmipp-3.1-foss-2015a-Python-2.7.9.eb | 32 +++++++++++++++++++ ... => Xmipp-3.1-intel-2015a-Python-2.7.9.eb} | 13 ++++++-- ...h => Xmipp-3.1_fix-library-includes.patch} | 0 ...ch => Xmipp-3.1_fix-sqlite-includes.patch} | 0 .../x/Xmipp/Xmipp_install-script.patch | 13 ++++++++ 5 files changed, 55 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb rename easybuild/easyconfigs/x/Xmipp/{Xmipp-3.1-intel-2015a.eb => Xmipp-3.1-intel-2015a-Python-2.7.9.eb} (64%) rename easybuild/easyconfigs/x/Xmipp/{library_imports.patch => Xmipp-3.1_fix-library-includes.patch} (100%) rename easybuild/easyconfigs/x/Xmipp/{sqlite_imports.patch => Xmipp-3.1_fix-sqlite-includes.patch} (100%) create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..3d82992342 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +name = 'Xmipp' +version = '3.1' + +homepage = 'http://xmipp.cnb.csic.es/' +description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2015a'} + +patches = [ + 'Xmipp-%(version)s_fix-sqlite-includes.patch', + 'Xmipp-%(version)s_fix-library-includes.patch', + 'Xmipp_install-script.patch', +] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Java', '1.8.0_40', '', True), + ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py + ('LibTIFF', '4.0.4beta'), + ('HDF5', '1.8.14'), + ('libjpeg-turbo', '1.4.0'), + ('FFTW', '3.3.4'), + ('SQLite', '3.8.8.1'), # must match SQLite used by Python + ('matplotlib', '1.4.3', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb similarity index 64% rename from easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb index 0f9bc0fa5f..82d76eef0e 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb @@ -9,17 +9,24 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'intel', 'version': '2015a'} -patches = ['sqlite_imports.patch', 'library_imports.patch'] +patches = [ + 'Xmipp-%(version)s_fix-sqlite-includes.patch', + 'Xmipp-%(version)s_fix-library-includes.patch', + 'Xmipp_install-script.patch', +] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver dependencies = [ ('Java', '1.8.0_40', '', True), - ('Python', '2.7.9'), # should have a working sqlite, and provide numpy - ('freetype', '2.5.5'), + ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), ('libjpeg-turbo', '1.4.0'), ('FFTW', '3.3.4'), ('SQLite', '3.8.8.1'), # must match SQLite used by Python + ('matplotlib', '1.4.3', versionsuffix), ] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/library_imports.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-library-includes.patch similarity index 100% rename from easybuild/easyconfigs/x/Xmipp/library_imports.patch rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-library-includes.patch diff --git a/easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-sqlite-includes.patch similarity index 100% rename from easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-sqlite-includes.patch diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch new file mode 100644 index 0000000000..c79477e52b --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch @@ -0,0 +1,13 @@ +--- install.sh.orig 2014-04-03 10:46:46.000000000 +0300 ++++ install.sh 2015-06-17 10:09:32.000000000 +0300 +@@ -820,8 +820,8 @@ + DO_PYTHON=1 + DO_PYMOD=1 + elif [ "${WITH_PYTHON}" = "false" ]; then +- DO_PYTHON=1 +- DO_PYMOD=1 ++ DO_PYTHON=0 ++ DO_PYMOD=0 + else + echoRed "Parameter --python only accept true or false values. Ignored and assuming default value." + fi -- GitLab From 4f2f3dc7bd35b80c5dc8c4e8c6fa80f6c3470da0 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 15:21:02 +0200 Subject: [PATCH 775/992] add bzip2 and Tcl goolf-1.7.20 dependencies --- .../b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb | 15 +++++++++++ .../t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb | 25 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb new file mode 100644 index 0000000000..ddcc6fecd4 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically +compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical +compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s/'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb new file mode 100644 index 0000000000..41060701af --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From be641b171fb4b3262ed87bdf06dec77a8f96ca5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 15:22:32 +0200 Subject: [PATCH 776/992] {vis}[goolf/1.4.10] Xmipp 3.1 --- .../Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb new file mode 100644 index 0000000000..7318afff3e --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -0,0 +1,16 @@ +name = 'Xmipp' +version = '3.1' +versionsuffix = '-with-incl-deps' + +homepage = 'http://xmipp.cnb.csic.es/' +description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# note: all other dependencies are taken care of by Xmipp itself +dependencies = [('Java', '1.8.0_40', '', True)] + +moduleclass = 'vis' -- GitLab From 184a2db03b94d8ba511a524269dff58c3acd5053 Mon Sep 17 00:00:00 2001 From: npklein Date: Wed, 17 Jun 2015 15:29:45 +0200 Subject: [PATCH 777/992] add dependencies libffi and gettext goolf-1.7.20 --- .../g/gettext/gettext-0.19.2-goolf-1.7.20.eb | 18 +++++++++++++++ .../l/libffi/libffi-3.1-goolf-1.7.20.eb | 23 +++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..55016086e0 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.2' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000..c0ec3f2067 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 5f300753aeee98712f01a55636d1d38d2629aff8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jun 2015 15:29:55 +0200 Subject: [PATCH 778/992] add missing easyconfigs, fix FFTW dep in Xmipp easyconfig for foss/2015a --- .../h/HDF5/HDF5-1.8.14-foss-2015a.eb | 51 ++++++++++++++++ .../l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb | 60 +++++++++++++++++++ .../Xmipp-3.1-foss-2015a-Python-2.7.9.eb | 2 +- 3 files changed, 112 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb new file mode 100644 index 0000000000..c3c747459d --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb @@ -0,0 +1,51 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_11-02-41 +name = 'HDF5' +version = "1.8.14" + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.2.0dev", + "easybuild-easyblocks_version": "2.2.0dev", + "timestamp": 1434441761, + "build_time": 176.49, + "install_size": 31544778, + "command_line": ['--buildpath=/tmp/hoste/easybuild_build', '--debug', '--installpath=/homeappl/home/hoste/appl_taito', '--modules-tool=Lmod', '--prefix=/wrk/hoste/EasyBuild', '--repositorypath=/wrk/hoste/EasyBuild/ebfiles_repo', '--robot=/homeappl/home/hoste/EasyBuild/easybuild-easyconfigs/easybuild/easyconfigs', '--sourcepath=/wrk/hoste/EasyBuild/sources', '--try-software-version=1.8.14', 'HDF5-1.8.13-foss-2015a.eb'], + "modules_tool": ('Lmod', '/appl/opt/lmod/5.9.4.1/lmod/lmod/libexec/lmod', '5.9.4'), + "core_count": 16, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", + "cpu_speed": 2600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2 --with-local-prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "taito-login4.csc.fi", + "os_name": "RHEL", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Nov 21 2013, 10:50:32) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb new file mode 100644 index 0000000000..025b0d6e1a --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb @@ -0,0 +1,60 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +# misleading name, this is a 'stable' release +version = '4.0.4beta' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.2.0dev", + "easybuild-easyblocks_version": "2.2.0dev", + "timestamp": 1434441102, + "build_time": 62.66, + "install_size": 4614536, + "command_line": ['--buildpath=/tmp/hoste/easybuild_build', '--debug', '--installpath=/homeappl/home/hoste/appl_taito', '--modules-tool=Lmod', '--prefix=/wrk/hoste/EasyBuild', '--repositorypath=/wrk/hoste/EasyBuild/ebfiles_repo', '--robot=/homeappl/home/hoste/EasyBuild/easybuild-easyconfigs/easybuild/easyconfigs', '--sourcepath=/wrk/hoste/EasyBuild/sources', '--try-toolchain="[\'foss\', \'2015a\']"', 'Xmipp-3.1-intel-2015a.eb'], + "modules_tool": ('Lmod', '/appl/opt/lmod/5.9.4.1/lmod/lmod/libexec/lmod', '5.9.4'), + "core_count": 16, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", + "cpu_speed": 2600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2 --with-local-prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "taito-login4.csc.fi", + "os_name": "RHEL", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Nov 21 2013, 10:50:32) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb index 3d82992342..fc928c6c57 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -24,7 +24,7 @@ dependencies = [ ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), ('libjpeg-turbo', '1.4.0'), - ('FFTW', '3.3.4'), + ('FFTW', '3.3.4', '', ('gompi', '2015a')), ('SQLite', '3.8.8.1'), # must match SQLite used by Python ('matplotlib', '1.4.3', versionsuffix), ] -- GitLab From 160836570895f4931dd6a62e25b6038c3717d599 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 15:48:10 +0200 Subject: [PATCH 779/992] Cosmetics and added checksums --- .../c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb | 17 ++++++++++---- .../c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 19 +++++++++++---- .../c/Cube/Cube-4.2.3-goolf-1.5.14.eb | 8 +++++-- .../easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb | 23 +++++++++++-------- .../c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb | 17 ++++++++++---- 5 files changed, 58 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb index b1b5830754..94eaf15f8d 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb @@ -1,11 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'ConfigureMake' name = "Cube" @@ -20,9 +24,12 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://apps.fz-juelich.de/scalasca/releases/cube/3.4/dist/cube-3.4.3.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/3.4/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + '703d4681851a5abf50946868f05e8f9e', # cube-3.4.3.tar.gz +] dependencies = [('Qt', '4.8.4')] diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index 941a048ad1..7159c84d00 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# Authors:: Markus Geimer -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -30,16 +33,22 @@ patches = [ 'Cube-4.2_fix-with-qt-check.patch', ] +checksums = [ + 'aa1b1594bacddd3a1931f9a9dea23ce8', # cube-4.2.tar.gz + 'da69fe49d347dc7722c30bb785106d96', # Cube-4.2_fix-Qt-version-check.patch + '5a746d4f6f4eb5eb8b464ca355b46891', # Cube-4.2_fix-with-qt-check.patch +] + dependencies = [('Qt', '4.8.4')] # The Cube Java reader is currently only used by TAU, which ships it's own # copy as a jar file. If you really want to enable it, make sure to set -# 'maxparallel=1', as automake's Java support is has difficulties handling +# 'maxparallel=1', as automake's Java support has difficulties handling # parallel builds. configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb index b4f0251684..7bda257ed2 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -21,16 +21,20 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +checksums = [ + '8f95b9531f5a8f8134f279c2767c9b20', # cube-4.2.3.tar.gz +] + dependencies = [('Qt', '4.8.4')] # The Cube Java reader is currently only used by TAU, which ships it's own # copy as a jar file. If you really want to enable it, make sure to set -# 'maxparallel=1', as automake's Java support is has difficulties handling +# 'maxparallel=1', as automake's Java support has difficulties handling # parallel builds. configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb index c0a4d9c729..01eebc5f7e 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -1,11 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -29,14 +33,15 @@ checksums = [ dependencies = [('Qt', '4.8.6')] +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support has difficulties handling +# parallel builds. +configopts = "--without-java-reader" + sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } -# If all prerequisites for the Cube Java reader are available on the system, -# parallel builds will fail. Alternatively, disable the Java reader using -# configopts = "--without-java-reader" -maxparallel = 1 - moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb index 0a2aec777e..560d4ea5c5 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# Authors:: Markus Geimer -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -24,16 +27,20 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +checksums = [ + 'ed4d6f3647eefa65fc194b5d1a5f4ffe', # cube-4.3.tar.gz +] + dependencies = [('Qt', '4.8.4')] # The Cube Java reader is currently only used by TAU, which ships it's own # copy as a jar file. If you really want to enable it, make sure to set -# 'maxparallel=1', as automake's Java support is has difficulties handling +# 'maxparallel=1', as automake's Java support has difficulties handling # parallel builds. configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } -- GitLab From 639239fcb05b2a8116b2371cde76a3713bcf5f55 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 Jun 2015 15:48:28 +0200 Subject: [PATCH 780/992] Add easyconfig for latest release which no longer includes Java reader --- .../c/Cube/Cube-4.3.2-foss-2015a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb new file mode 100644 index 0000000000..b12da485bc --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = "Cube" +version = "4.3.2" + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + 'a9119524df5a39e7a5bf6dee4de62e30', # cube-4.3.2.tar.gz +] + +dependencies = [('Qt', '4.8.6')] + +sanity_check_paths = { + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' -- GitLab From 5bcead1e283193bdd88aacbee2ec931ea0d0a708 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:11:50 +0200 Subject: [PATCH 781/992] leading space --- .../easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb index 55016086e0..b9b28dda44 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb @@ -5,8 +5,8 @@ version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may -build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools -and documentation""" + build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools + and documentation""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -- GitLab From 31abb3bac4d92482ed63daf9f0286a9a4997314b Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:12:35 +0200 Subject: [PATCH 782/992] leading space --- easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb index c0ec3f2067..bb8ee020a7 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb @@ -4,8 +4,8 @@ name = 'libffi' version = '3.1' homepage = 'http://sourceware.org/libffi/' -description = """The libffi library provides a portable, high level programming interface to various calling -conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + description = """The libffi library provides a portable, high level programming interface to various calling + conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -- GitLab From f61c083dc61b1843d20c4677f34cb3d86e11ede5 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:14:49 +0200 Subject: [PATCH 783/992] leading space, align with common dependencies --- .../easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb index e57987a01a..3638dbedbc 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb @@ -5,8 +5,8 @@ version = '1.12.18' homepage = 'http://cairographics.org' description = """Cairo is a 2D graphics library with support for multiple output devices. -Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, -PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" toolchain = {'name': 'goolf', 'version': '1.7.20'} @@ -14,13 +14,13 @@ source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_XZ] dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), ('libpng', '1.6.12'), ('freetype', '2.5.3'), - ('zlib', '1.2.8'), ('pixman', '0.32.6'), ('fontconfig', '2.11.1'), ('expat', '2.1.0'), - ('bzip2', '1.0.6'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -- GitLab From 9ddfed122fd50b3d218baaef796138b344a25675 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Wed, 17 Jun 2015 17:26:25 +0200 Subject: [PATCH 784/992] fix wrong indent --- easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb index bb8ee020a7..ba1db82dae 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb @@ -4,7 +4,7 @@ name = 'libffi' version = '3.1' homepage = 'http://sourceware.org/libffi/' - description = """The libffi library provides a portable, high level programming interface to various calling +description = """The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -- GitLab From e5f696794565f468ed58d137e93e81c73b54ca32 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Thu, 18 Jun 2015 09:11:11 +0200 Subject: [PATCH 785/992] leading space, dependencies moved below sources --- easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb index 72296e698f..eb194cd37c 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb @@ -5,7 +5,7 @@ version = '3.6' homepage = 'http://sourceforge.net/projects/snpeff/' description = """SnpEff is a variant annotation and effect prediction tool. -It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -13,11 +13,11 @@ java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver)] - source_urls = [SOURCEFORGE_SOURCE] sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] +dependencies = [(java, javaver)] + checksums = ['f4571413833df913261ff76b6f40bb76'] sanity_check_paths = { -- GitLab From 32292e9427b0030b3c9403bd03314e16faca83b2 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Thu, 18 Jun 2015 09:11:34 +0200 Subject: [PATCH 786/992] lead --- easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb index 7e0c5d595f..8b1570a181 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb @@ -5,7 +5,7 @@ version = '4.1d' homepage = 'http://sourceforge.net/projects/snpeff/' description = """SnpEff is a variant annotation and effect prediction tool. -It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" toolchain = {'name': 'dummy', 'version': 'dummy'} @@ -13,11 +13,11 @@ java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver)] - source_urls = [SOURCEFORGE_SOURCE] sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] +dependencies = [(java, javaver)] + checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] sanity_check_paths = { -- GitLab From 56cf9da32ad909f325a150a28facfe0a2f820f6f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jun 2015 10:14:38 +0200 Subject: [PATCH 787/992] fix PyPI URLs: use https --- .../Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015.05.eb | 12 ++++++------ .../Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index 08f3c850f6..5b829d6a73 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.22' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index e5b95d6f14..3290f94dba 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,13 +46,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb index 28482a1b30..335241b807 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb @@ -9,7 +9,7 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +source_urls = ['https://pypi.python.org/packages/source/T/%s' % name] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb index e95fac6936..a9aa394aab 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb @@ -9,7 +9,7 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +source_urls = ['https://pypi.python.org/packages/source/T/%s' % name] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From 7b78b8c68555e2713d89479e296699758f97c03a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jun 2015 11:20:29 +0200 Subject: [PATCH 788/992] {vis}[foss/2015a] SPIDER 22.10 --- .../s/SPIDER/SPIDER-22.10-foss-2015a.eb | 40 +++++++++++++++++++ .../s/SPIDER/SPIDER-22.10_gfortran49.patch | 22 ++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb new file mode 100644 index 0000000000..31a4eb409a --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'static': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = [ + 'SPIDER-%(version)s_fix-syntax-ifort.patch', + 'SPIDER-%(version)s_gfortran49.patch', +] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_GFORTRAN -cpp -dM -c" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch new file mode 100644 index 0000000000..3ffd041738 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch @@ -0,0 +1,22 @@ +--- spider/src/copy1.f.orig 2015-06-16 18:11:37.000000000 +0300 ++++ spider/src/copy1.f 2015-06-16 18:12:12.000000000 +0300 +@@ -72,6 +72,8 @@ + INTEGER, PARAMETER :: LUNXM1 = 83 + INTEGER, PARAMETER :: LUNXM2 = 84 + ++ LOGICAL :: VERBOSET ++ + C FROM/'AS','MR','PD','RA','NI','TE','VA','EM','NT','XP'/ + + C TO/'AS','BR','MR','PO','RA','TI','XP','OP','JPG'/ +--- spider/src/pr3d.f.orig 2015-06-16 18:49:45.000000000 +0300 ++++ spider/src/pr3d.f 2015-06-16 18:50:05.000000000 +0300 +@@ -75,7 +75,7 @@ + + CALL SET_MPI(ICOMM,MYPID,MPIERR) + +- WANTSQRTS = (FSCOP == .TRUE.) ++ WANTSQRTS = (FSCOP .eqv. .TRUE.) + + C INPUT FIRST IMAGE + MAXIM = 0 -- GitLab From 1c5365d353a6ec6f3243cd9edad6f819816f1d5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jun 2015 11:42:08 +0200 Subject: [PATCH 789/992] use Java 1.7 as dep in Xmipp 3.1 easyconfig --- .../x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb index 7318afff3e..c1f4fa485c 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -11,6 +11,6 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'goolf', 'version': '1.4.10'} # note: all other dependencies are taken care of by Xmipp itself -dependencies = [('Java', '1.8.0_40', '', True)] +dependencies = [('Java', '1.7.0_80', '', True)] moduleclass = 'vis' -- GitLab From 84842c86f6c7892fb05912715197176fcd38f933 Mon Sep 17 00:00:00 2001 From: npklein Date: Thu, 18 Jun 2015 15:51:30 +0200 Subject: [PATCH 790/992] readd .eb file after accidentally syncing it out --- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 116 ++++++++++++++++++ 1 file changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb new file mode 100644 index 0000000000..2eabb347c9 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -0,0 +1,116 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'https://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), + #('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('https://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/ '], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + + +moduleclass = 'lang' -- GitLab From a24cf6c099160dfc700f1e35cb9ca10d10e15e84 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 19 Jun 2015 10:37:00 +0200 Subject: [PATCH 791/992] Add Tk --- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index 2eabb347c9..c011298dc9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), #('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -- GitLab From 2f000ca752464e850fc7e35985cf06edc4e5cede Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 19 Jun 2015 10:53:15 +0200 Subject: [PATCH 792/992] add dependency Tk-8.6.3-goolf-1.7.20-no0X11 --- .../t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb new file mode 100644 index 0000000000..025f5e6476 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From ff2d728913db076780847346429d6e6adecd78e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 15:29:07 +0200 Subject: [PATCH 794/992] {tools}[foss+intel/2015a] bibtexparser 0.5 + 0.6.0 --- ...ibtexparser-0.5-foss-2015a-Python-2.7.9.eb | 20 +++++++++++++++++++ ...btexparser-0.5-intel-2015a-Python-2.7.9.eb | 20 +++++++++++++++++++ ...texparser-0.6.0-foss-2015a-Python-2.7.9.eb | 20 +++++++++++++++++++ ...exparser-0.6.0-intel-2015a-Python-2.7.9.eb | 20 +++++++++++++++++++ 4 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..383c7de16a --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.5' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..4c591a3fc0 --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.5' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..7060a6e07d --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.6.0' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..88ee53e88a --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.6.0' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' -- GitLab From 4917b5409021d8750177ef477da4dd4a76d460db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 15:51:12 +0200 Subject: [PATCH 795/992] style fix in OpenMPI easyconfigs --- .../o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb | 5 ++--- .../easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb | 5 ++--- .../easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 5 ++--- .../o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 9 +++------ .../o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 7 +++---- .../o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 9 ++++----- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 7 ++++--- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 7 +++---- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 7 +++---- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 7 +++---- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 9 +++------ .../OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 10 +++------- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 9 +++------ .../easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 6 ++---- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 6 ++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb | 6 ++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb | 6 ++---- .../OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 6 ++---- .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 6 ++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 6 ++---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb | 6 ++---- .../OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 6 ++---- .../OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 6 ++---- .../o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 6 ++---- 29 files changed, 75 insertions(+), 122 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb index e568f8411e..e2dcab157e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb @@ -17,11 +17,10 @@ patches = ['pax_disable.patch'] configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb index fe72e01efd..af837e0815 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb @@ -17,11 +17,10 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index a53d8baacf..c95534677f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -26,11 +26,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 3f5d4cafd7..6c869405ae 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.6')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", "otf", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 68114cf721..9efd057826 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 109447fa55..5eadff7219 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 983eb22945..6d4df930a7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,15 +19,14 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 7d3922cea0..653bf81122 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 21bd882ac7..9a90f6103b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,12 +24,13 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", - "mpif-mpi-io", "mpi", "mpi_portable_platform"]], + "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 90dc3e3449..72d77b0d4b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -18,12 +18,11 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index 5e9b5fcda8..a762cb5756 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -18,12 +18,11 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 394c231617..2e51419ed1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -20,12 +20,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 6cac76d97d..380ed604f3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -21,12 +21,11 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 908f092bfa..16d67f2c01 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -23,12 +23,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index c9d45613df..6efbf16c1c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -23,12 +23,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 85b6644c9f..219134b916 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 4d2c94f271..4c2e264500 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,18 +18,14 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' - diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 79c31e1c3d..a29d619ce5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 1f4d38649b..6687a0ffa0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -23,12 +23,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index fdf4f47fc8..3e20609bc6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -31,12 +31,10 @@ configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --d # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index d9eca98720..eeb7c2fe82 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index fb7afbbd41..a47fa4f0f1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index e1057430c2..c6c6f0c9ab 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -20,12 +20,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.9')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index f73d19d32c..39b44f0df0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -22,12 +22,10 @@ dependencies = [('hwloc', '1.9')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 3841ad29d2..2eb439ac34 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index e90682df3b..e009a63259 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index a3c918320f..780c3c78ba 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -22,12 +22,10 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index d7df86c8d6..ca0afea9dc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -23,12 +23,10 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb index 17455567fb..095d22d991 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } -- GitLab From 5a802805e9a499b8fd1b054a6957581d2ba0cc8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 16:07:40 +0200 Subject: [PATCH 796/992] fix syntax issues --- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 2 +- 15 files changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 6c869405ae..d88a606fa0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -24,7 +24,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 9efd057826..63ad283770 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -25,7 +25,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 5eadff7219..6562c8883f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -25,7 +25,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 6d4df930a7..0d984429f3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -23,7 +23,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 653bf81122..1c96459eb6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -25,7 +25,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 9a90f6103b..825a5a7a0c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -28,7 +28,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 72d77b0d4b..2501ef80eb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -22,7 +22,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index a762cb5756..a58e7c5d7e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -22,7 +22,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 2e51419ed1..c542435f08 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -24,7 +24,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 380ed604f3..4628f0030f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -25,7 +25,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 16d67f2c01..8106b6d183 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -27,7 +27,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index 6efbf16c1c..16eab6b12c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -27,7 +27,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 219134b916..33b34df331 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -24,7 +24,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 4c2e264500..19ad55fe18 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -22,7 +22,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index a29d619ce5..9c2f4e66f1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -24,7 +24,7 @@ libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "o "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], -- GitLab From 15e3c190fe31987971b783e207dffe180aced312 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 16:59:59 +0200 Subject: [PATCH 797/992] remove buildstats that snuck in --- .../fontconfig-2.11.1-intel-2015a.eb | 2 +- .../h/HDF5/HDF5-1.8.14-foss-2015a.eb | 25 ------------------- .../l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb | 25 ------------------- 3 files changed, 1 insertion(+), 51 deletions(-) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb index a8f2612b6a..54455c5111 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('expat', '2.1.0'), - ('freetype','2.5.5'), + ('freetype', '2.5.5'), ] configopts = '--disable-docs ' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb index c3c747459d..35077bfe35 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb @@ -24,28 +24,3 @@ dependencies = [ ] moduleclass = 'data' - -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.2.0dev", - "easybuild-easyblocks_version": "2.2.0dev", - "timestamp": 1434441761, - "build_time": 176.49, - "install_size": 31544778, - "command_line": ['--buildpath=/tmp/hoste/easybuild_build', '--debug', '--installpath=/homeappl/home/hoste/appl_taito', '--modules-tool=Lmod', '--prefix=/wrk/hoste/EasyBuild', '--repositorypath=/wrk/hoste/EasyBuild/ebfiles_repo', '--robot=/homeappl/home/hoste/EasyBuild/easybuild-easyconfigs/easybuild/easyconfigs', '--sourcepath=/wrk/hoste/EasyBuild/sources', '--try-software-version=1.8.14', 'HDF5-1.8.13-foss-2015a.eb'], - "modules_tool": ('Lmod', '/appl/opt/lmod/5.9.4.1/lmod/lmod/libexec/lmod', '5.9.4'), - "core_count": 16, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", - "cpu_speed": 2600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2 --with-local-prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "taito-login4.csc.fi", - "os_name": "RHEL", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Nov 21 2013, 10:50:32) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb index 025b0d6e1a..accbb2bb0a 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb @@ -33,28 +33,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.2.0dev", - "easybuild-easyblocks_version": "2.2.0dev", - "timestamp": 1434441102, - "build_time": 62.66, - "install_size": 4614536, - "command_line": ['--buildpath=/tmp/hoste/easybuild_build', '--debug', '--installpath=/homeappl/home/hoste/appl_taito', '--modules-tool=Lmod', '--prefix=/wrk/hoste/EasyBuild', '--repositorypath=/wrk/hoste/EasyBuild/ebfiles_repo', '--robot=/homeappl/home/hoste/EasyBuild/easybuild-easyconfigs/easybuild/easyconfigs', '--sourcepath=/wrk/hoste/EasyBuild/sources', '--try-toolchain="[\'foss\', \'2015a\']"', 'Xmipp-3.1-intel-2015a.eb'], - "modules_tool": ('Lmod', '/appl/opt/lmod/5.9.4.1/lmod/lmod/libexec/lmod', '5.9.4'), - "core_count": 16, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz", - "cpu_speed": 2600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2 --with-local-prefix=/homeappl/home/hoste/appl_taito/software/GCC/4.9.2; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "taito-login4.csc.fi", - "os_name": "RHEL", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Nov 21 2013, 10:50:32) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/homeappl/home/hoste/appl_taito/software/GCC/4.9.2/bin/gcc", - "system_python_path": "/usr/bin/python", -}] -- GitLab From a52548e1f0a804fa6339ede3b322fb7ffd3997e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 17:44:44 +0200 Subject: [PATCH 798/992] {tools}[intel/2015a] IPython 3.2.3 --- .../IPython-3.1.0-intel-2015a-Python-2.7.9.eb | 2 +- .../IPython-3.2.3-intel-2015a-Python-2.7.9.eb | 42 +++++++++++++++++++ ...MQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb | 33 +++++++++++++++ ...requests-2.7.0-intel-2015a-Python-2.7.9.eb | 29 +++++++++++++ 4 files changed, 105 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb index 377e678904..f7ad35c7e1 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb @@ -18,7 +18,7 @@ source_urls = ['http://archive.ipython.org/release/%(version)s/'] python = 'Python' pyver = '2.7.9' -pyshortver = '2.7' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..e3beaf3595 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,42 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.2.3' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://archive.ipython.org/release/%(version)s/'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('requests', '2.7.0', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', '') + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000..0986a01c06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.7.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '3.2.5' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f8a41a318c --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], +} + +moduleclass = 'devel' -- GitLab From 662bee79fd88155cfe1b48fd9a54c9a901bd7e85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 17:46:30 +0200 Subject: [PATCH 799/992] {tools}[foss/2015a] IPython 3.2.3 --- ...IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../IPython-3.2.3-foss-2015a-Python-2.7.9.eb | 42 +++++++++++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb | 27 ++++++++++++ ...ZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb | 33 +++++++++++++++ .../Pygments-2.0.2-foss-2015a-Python-2.7.9.eb | 29 +++++++++++++ .../pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb | 32 ++++++++++++++ .../requests-2.7.0-foss-2015a-Python-2.7.9.eb | 29 +++++++++++++ .../util-linux-2.26.1-foss-2015a.eb | 33 +++++++++++++++ .../z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb | 34 +++++++++++++++ 9 files changed, 260 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb index 3c52ea836c..be492fa165 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -18,7 +18,7 @@ source_urls = ['http://archive.ipython.org/release/%(version)s/'] python = 'Python' pyver = '2.7.3' -pyshortver = '2.7' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..96b5821500 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,42 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.2.3' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://archive.ipython.org/release/%(version)s/'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('requests', '2.7.0', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', '') + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb new file mode 100644 index 0000000000..6dae1dce85 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000..fca9d5270f --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.7.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '3.2.5' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..103bb38998 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.0.2' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..27ca7fc128 --- /dev/null +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'pysqlite' +version = '2.6.3' + +homepage = 'https://pypi.python.org/pypi/pysqlite' +description = """pysqlite is an interface to the SQLite 3.x embedded relational database engine. + It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SQLite', '3.8.8.1'), # also dependency for Python itself +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +options = {'modulename': '%(name)s%(version_major)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..d4e3a34ddb --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb new file mode 100644 index 0000000000..dc874b1a62 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.26.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = '--disable-chfn-chsh --disable-login --disable-su ' +configopts += '--disable-wall --disable-use-tty-group ' +configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb new file mode 100644 index 0000000000..537ac748fe --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '3.2.5' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.26.1'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 49bb0438d2fcd6a5192c3440dc1ea693d540bf28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 17:48:04 +0200 Subject: [PATCH 800/992] {devel}[*/2015a] Boost 1.5.8.0 w/ Python 2.7.10 --- .../Boost-1.58.0-foss-2015a-Python-2.7.10.eb | 25 +++++++++++++++++++ .../Boost-1.58.0-intel-2015a-Python-2.7.10.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..76622b0263 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..d48f0872dd --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 1c0d6839ddd3a32938ffa015eb61737275576c70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 17:48:37 +0200 Subject: [PATCH 801/992] {data}[*/2015a] HDF5 1.8.15-patch1 --- .../h/HDF5/HDF5-1.8.15-foss-2015a.eb | 23 ++++++++++++++++ .../h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb | 23 ++++++++++++++++ .../h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb | 26 +++++++++++++++++++ 3 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb new file mode 100644 index 0000000000..ef7549e987 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.15' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb new file mode 100644 index 0000000000..a9ec210198 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb new file mode 100644 index 0000000000..ec9b5d3a8a --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From 8cb2351f31b92d82dce6580016c863c09cb33fbc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 18:16:51 +0200 Subject: [PATCH 802/992] fix change in sanity check paths for OpenMPI 1.6.4 and 1.6.5 --- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 4 ++-- .../OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 4 ++-- 14 files changed, 28 insertions(+), 28 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 63ad283770..b42d9a8b03 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,8 +21,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 6562c8883f..fc479108fe 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,8 +21,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 0d984429f3..8b588833b0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,8 +19,8 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 1c96459eb6..168f6f9d23 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,8 +21,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 825a5a7a0c..933369e32b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,8 +24,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 2501ef80eb..7c0a81dc4a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -18,8 +18,8 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index a58e7c5d7e..125d5b989d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -18,8 +18,8 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index c542435f08..aaa6f69c8d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -20,8 +20,8 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 4628f0030f..fcb341d4f3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -21,8 +21,8 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 8106b6d183..c3cb7f8713 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -23,8 +23,8 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index 16eab6b12c..125577dc71 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -23,8 +23,8 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 33b34df331..4fc8978e4d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,8 +20,8 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 19ad55fe18..0bb4349893 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,8 +18,8 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 9c2f4e66f1..e9f2f244ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,8 +20,8 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", - "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + -- GitLab From 0cb03e18fbd1985cb0b72dba6a485a12878fba11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 18:43:23 +0200 Subject: [PATCH 803/992] {vis}[*/2015a] PyQt 4.11.4 --- .../PyQt-4.11.4-foss-2015a-Python-2.7.9.eb | 36 +++++++++++++++++++ .../PyQt-4.11.4-intel-2015a-Python-2.7.9.eb | 36 +++++++++++++++++++ .../SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb | 25 +++++++++++++ .../SIP-4.16.8-intel-2015a-Python-2.7.9.eb | 25 +++++++++++++ 4 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..34baa22804 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.4' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +pythonshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --no-sip-files" + +options = {'modulename': 'PyQt4'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..789bf13b2c --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.4' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +pythonshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --no-sip-files" + +options = {'modulename': 'PyQt4'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..e745733edd --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.8' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +configopts = "configure.py" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..87b18fbf3c --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.8' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +configopts = "configure.py" + +moduleclass = 'lang' -- GitLab From 8fdf2e62a4bbed665e4d9df06c77b939548aba04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 20:14:48 +0200 Subject: [PATCH 804/992] correct IPython version to 3.2.0 --- ...Python-2.7.9.eb => IPython-3.2.0-foss-2015a-Python-2.7.9.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/i/IPython/{IPython-3.2.3-foss-2015a-Python-2.7.9.eb => IPython-3.2.0-foss-2015a-Python-2.7.9.eb} (98%) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb similarity index 98% rename from easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb index 96b5821500..c15643b57e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = "PythonPackage" name = 'IPython' -version = '3.2.3' +version = '3.2.0' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: -- GitLab From 2beb46eb0f0fa694489751f090d4299c95ec6090 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 20:15:34 +0200 Subject: [PATCH 805/992] correct IPython version to 3.2.0 --- ...ython-2.7.9.eb => IPython-3.2.0-intel-2015a-Python-2.7.9.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/i/IPython/{IPython-3.2.3-intel-2015a-Python-2.7.9.eb => IPython-3.2.0-intel-2015a-Python-2.7.9.eb} (98%) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb similarity index 98% rename from easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb index e3beaf3595..5494f4a74f 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = "PythonPackage" name = 'IPython' -version = '3.2.3' +version = '3.2.0' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: -- GitLab From 6539abef5d240218e11f6102b69699fa837e9b49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 22:38:46 +0200 Subject: [PATCH 806/992] add PyPI source URL for IPython --- .../i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb index 5494f4a74f..5b0893e10b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb @@ -14,7 +14,10 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.9' -- GitLab From a79e01150c3db6ca87c8d5e13ca1edbaeb6a1987 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 22:39:40 +0200 Subject: [PATCH 807/992] add PyPI source URL for IPython --- .../i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb | 5 ++++- .../i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb index be492fa165..92f605169b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -14,7 +14,10 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb index c15643b57e..ca831cfe27 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb @@ -14,7 +14,10 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.9' -- GitLab From 0ff8e2b924ff001f2a4a83b622caa3cba84e260f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 22:40:33 +0200 Subject: [PATCH 808/992] add PyPI source URL for IPython 3.1.0 --- .../i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb index f7ad35c7e1..4ddce0d142 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb @@ -14,7 +14,10 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.9' -- GitLab From 9f197374adf6f9fa897b2f2660fa2150b3da80a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Jun 2015 22:45:08 +0200 Subject: [PATCH 809/992] add patch for Qt 4.8.6 with intel/2015a --- .../easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb | 5 ++++- .../easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch | 15 +++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb index 7ca9946d90..1ab132124a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb @@ -12,7 +12,10 @@ source_urls = [ ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -patches = ['Qt-4.8.6_icc-qUnused.patch'] +patches = [ + 'Qt-%(version)s_icc-qUnused.patch', + 'Qt-%(version)s_phonon-export.patch', +] dependencies = [('GLib', '2.40.0')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch b/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch new file mode 100644 index 0000000000..4170411ac1 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch @@ -0,0 +1,15 @@ +fixed for error "undefined reference to `vtable for Phonon::ObjectDescriptionModel<(Phonon::ObjectDescriptionType)0>'" +that occurs (only) on some systems (e.g. RHEL6/Sandy Bridge) +based on https://forum.qt.io/topic/35044/build-failure-4-8-5-on-mac-with-phonon/9 +author: Kenneth Hoste (HPC-UGent) +--- qt-everywhere-opensource-src-4.8.6/src/3rdparty/phonon/phonon/objectdescriptionmodel.h.orig 2015-06-22 23:18:54.723573581 +0300 ++++ qt-everywhere-opensource-src-4.8.6/src/3rdparty/phonon/phonon/objectdescriptionmodel.h 2015-06-22 23:19:16.902399019 +0300 +@@ -141,7 +141,7 @@ + + /* Required to ensure template class vtables are exported on both symbian + and existing builds. */ +-#if (defined(Q_OS_SYMBIAN) && defined(Q_CC_RVCT)) || defined(Q_CC_CLANG) ++#if (defined(Q_OS_SYMBIAN) && defined(Q_CC_RVCT)) || defined(Q_CC_CLANG) || defined(Q_CC_INTEL) + // RVCT compiler (2.2.686) requires the export declaration to be on the class to export vtables + // MWC compiler works both ways + // GCCE compiler is unknown (it can't compile QtCore yet) -- GitLab From c1d5caa98cdce1a88eb94ca8058978bd285ef085 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 11:15:41 +0200 Subject: [PATCH 810/992] add M4 as build dep for GCC 5.1.0 --- .../g/GCC/GCC-5.1.0-binutils-2.25.eb | 5 +++- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 27 +++++++++++++++++++ 3 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index b9370c56ff..44330ce226 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -29,7 +29,10 @@ sources = [ 'isl-0.14.tar.bz2', ] -builddependencies = [('binutils', binutilsver)] +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', binutilsver), +] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 4968008ae8..9097cd1a47 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -28,6 +28,8 @@ sources = [ patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +builddependencies = [('M4', '1.4.17')] + checksums = [ 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb new file mode 100644 index 0000000000..9c1b1f5017 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. +It is mostly SVR4 compatible although it has some extensions +(for example, handling more than 9 positional parameters to macros). +GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['M4-%(version)s-no-gets.patch'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 3531d75cc20918188a3f98e6cc268f48f0c75a74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 11:26:37 +0200 Subject: [PATCH 811/992] remove unrequired patch in M4 1.4.17 easyconfig --- easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 9c1b1f5017..e76d5efa3d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -15,8 +15,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -patches = ['M4-%(version)s-no-gets.patch'] - configopts = "--enable-cxx" sanity_check_paths = { -- GitLab From f6d70f78a16b69afb8a3c90c3107cd75458bbaa3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 12:42:00 +0200 Subject: [PATCH 812/992] use empty version in dummy toolchain so dependencies get loaded --- easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index 44330ce226..8bbf0ea88e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -8,7 +8,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 9097cd1a47..a69c58da2c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' -- GitLab From 018f2c314563b66bb6dd770f097586ef87585595 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 13:28:11 +0200 Subject: [PATCH 813/992] {devel}[*/2015a] CMake 3.2.3 --- .../c/CMake/CMake-3.2.3-foss-2015a.eb | 22 +++++++++++++++++++ .../c/CMake/CMake-3.2.3-intel-2015a.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb new file mode 100644 index 0000000000..c7935c7c64 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb new file mode 100644 index 0000000000..f4cde92c3c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 18d49280a7c6b6ba740bbea1e9a4db57af06bac3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 13:56:59 +0200 Subject: [PATCH 814/992] style fix --- easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index e76d5efa3d..3f396ce26b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -5,9 +5,9 @@ version = '1.4.17' homepage = 'http://www.gnu.org/software/m4/m4.html' description = """GNU M4 is an implementation of the traditional Unix macro processor. -It is mostly SVR4 compatible although it has some extensions -(for example, handling more than 9 positional parameters to macros). -GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. + It is mostly SVR4 compatible although it has some extensions + (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From be2c6392f6a001b60a64c909afba2eefc2de7c88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 15:04:54 +0200 Subject: [PATCH 815/992] {vis}[*/2015a] freetype 2.6 --- .../f/freetype/freetype-2.6-foss-2015a.eb | 21 +++++++++++++++++++ .../f/freetype/freetype-2.6-intel-2015a.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb new file mode 100644 index 0000000000..3678616622 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb new file mode 100644 index 0000000000..6a1b7e739c --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' -- GitLab From 9721e2746dab0690179a0a14cab34631fde54a5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Jun 2015 15:51:29 +0200 Subject: [PATCH 816/992] {bio}[*/2015a] EMAN 2.11 --- .../EMAN2-2.11-foss-2015a-Python-2.7.9.eb | 44 +++++++++++++++++++ .../EMAN2-2.11-intel-2015a-Python-2.7.9.eb | 44 +++++++++++++++++++ .../l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb | 34 ++++++++++++++ .../l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb | 34 ++++++++++++++ 4 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f239ad58fc --- /dev/null +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'EMAN2' +version = '2.11' + +homepage = 'http://blake.bcm.edu/emanwiki/EMAN2' +description = """EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite + with a primary focus on processing data from transmission electron microscopes. """ + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://ncmi.bcm.edu/ncmi/software/counter_222/software_130/'] +sources = ['eman%(version)s.source.tar.gz'] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + # FFTW provided via toolchain + ('GSL', '1.16'), + ('Python', pyver), # also provides numpy + ('Boost', '1.58.0', versionsuffix), + ('IPython', '3.2.0', versionsuffix), + ('HDF5', '1.8.15-patch1'), + ('freetype', '2.6'), + # optional + ('PyQt', '4.11.4', versionsuffix), + ('LibTIFF', '4.0.4'), + ('libpng', '1.6.17'), +] +builddependencies = [('CMake', '3.2.3')] + +start_dir = 'eman2' +separate_build_dir = True + +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', + 'bin/e2filtertool.py'], + 'dirs': ['examples', 'include', 'lib', 'test/rt'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..b7a9c16a5a --- /dev/null +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'EMAN2' +version = '2.11' + +homepage = 'http://blake.bcm.edu/emanwiki/EMAN2' +description = """EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite + with a primary focus on processing data from transmission electron microscopes. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ncmi.bcm.edu/ncmi/software/counter_222/software_130/'] +sources = ['eman%(version)s.source.tar.gz'] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('FFTW', '3.3.4'), + ('GSL', '1.16'), + ('Python', pyver), # also provides numpy + ('Boost', '1.58.0', versionsuffix), + ('IPython', '3.2.0', versionsuffix), + ('HDF5', '1.8.15-patch1'), + ('freetype', '2.6'), + # optional + ('PyQt', '4.11.4', versionsuffix), + ('LibTIFF', '4.0.4'), + ('libpng', '1.6.17'), +] +builddependencies = [('CMake', '3.2.3')] + +start_dir = 'eman2' +separate_build_dir = True + +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', + 'bin/e2filtertool.py'], + 'dirs': ['examples', 'include', 'lib', 'test/rt'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb new file mode 100644 index 0000000000..70578c5f23 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb new file mode 100644 index 0000000000..6b0d237d17 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From d32f0dd08d8da1db6105daf58212d8808bd03a4f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 24 Jun 2015 00:58:20 +0200 Subject: [PATCH 817/992] Check for MPI-specific driver during sanity check --- .../v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb index b3fef1121f..b5fb8fcae1 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -34,7 +34,7 @@ checksums = [ install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { - 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf"], + 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf", "lib/vampirserver-driver.so"], 'dirs': [] } -- GitLab From e8350ce57e79a84d5d8474fb248c7bb2bd6a4ec1 Mon Sep 17 00:00:00 2001 From: umcg-mterpstra Date: Wed, 24 Jun 2015 16:19:20 +0200 Subject: [PATCH 818/992] created cramtools-v2.0-Java-1.7.0_80.eb --- .../cramtools/cramtools-v2.0-Java-1.7.0_80.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb new file mode 100644 index 0000000000..aab392a85f --- /dev/null +++ b/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb @@ -0,0 +1,27 @@ +name = 'cramtools' +version = '2.0' + +homepage = 'https://github.com/enasequence/cramtools/' +description = """CRAMTools is a set of Java tools and APIs for efficient compression of sequence read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +easyblock = 'Tarball' + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/enasequence/%(name)s/archive/'] + + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +modloadmsg = """To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/cramtools-2.0.jar""" + +sanity_check_paths = { + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': ["lib"] +} + +moduleclass = 'bio' -- GitLab From dc88b5311cf335f8e4dec1cd7e963ba8d33711b6 Mon Sep 17 00:00:00 2001 From: mmterpstra Date: Wed, 24 Jun 2015 17:14:23 +0200 Subject: [PATCH 819/992] Update cramtools-v2.0-Java-1.7.0_80.eb --- .../c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb index aab392a85f..19162420ed 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb @@ -1,17 +1,19 @@ +easyblock = 'Tarball' + name = 'cramtools' version = '2.0' homepage = 'https://github.com/enasequence/cramtools/' -description = """CRAMTools is a set of Java tools and APIs for efficient compression of sequence read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.""" +description = """CRAMTools is a set of Java tools and APIs for efficient compression of sequence +read data. Although this is intended as a stable version the code is released as +early access. Parts of the CRAMTools are experimental and may not be supported +in the future.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -easyblock = 'Tarball' -# download manually from http://www.broadinstitute.org/gatk/download sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/enasequence/%(name)s/archive/'] - java = 'Java' javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) -- GitLab From a0c410cbe64ba3f83295cc7b207d73f9e023f146 Mon Sep 17 00:00:00 2001 From: mmterpstra Date: Wed, 24 Jun 2015 17:22:23 +0200 Subject: [PATCH 820/992] Rename cramtools-v2.0-Java-1.7.0_80.eb to cramtools-2.0-Java-1.7.0_80.eb --- ...tools-v2.0-Java-1.7.0_80.eb => cramtools-2.0-Java-1.7.0_80.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/cramtools/{cramtools-v2.0-Java-1.7.0_80.eb => cramtools-2.0-Java-1.7.0_80.eb} (100%) diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb similarity index 100% rename from easybuild/easyconfigs/c/cramtools/cramtools-v2.0-Java-1.7.0_80.eb rename to easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb -- GitLab From 0c577d7bde6b4d557ced343a304501f98629982b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 09:10:10 +0200 Subject: [PATCH 821/992] trivial style fixes --- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb | 8 ++++---- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb | 8 ++++---- .../v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb index 62ddb26846..44f692903f 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -10,7 +10,7 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock='Binary' +easyblock = 'Binary' name = "Vampir" version = "8.4.1" @@ -27,6 +27,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { @@ -34,9 +37,6 @@ sanity_check_paths = { 'dirs': [] } -# Adjust this variable to point to the location of your Vampir license file -license_file = '/example/licenses/path/vampir.license' - modextravars = { 'VAMPIR_LICENSE': license_file, } diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb index 379ca0d9f4..5596a89f02 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -10,7 +10,7 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock='Binary' +easyblock = 'Binary' name = "Vampir" version = "8.4.1" @@ -30,6 +30,9 @@ checksums = [ '471840910cd552a5a788df3b69251d29', # vampir-8.4.1-linux-x86_64-setup.bin ] +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" sanity_check_paths = { @@ -37,9 +40,6 @@ sanity_check_paths = { 'dirs': [] } -# Adjust this variable to point to the location of your Vampir license file -license_file = '/example/licenses/path/vampir.license' - modextravars = { 'VAMPIR_LICENSE': license_file, } diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb index b5fb8fcae1..5b068e3cf7 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -10,7 +10,7 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock='Binary' +easyblock = 'Binary' name = "VampirServer" version = "8.4.1" @@ -31,6 +31,9 @@ checksums = [ '2a2236bb071168b7d488c83363c30ac8', # vampirserver-8.4.1-linux-x86_64-setup.bin ] +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" sanity_check_paths = { @@ -38,9 +41,6 @@ sanity_check_paths = { 'dirs': [] } -# Adjust this variable to point to the location of your Vampir license file -license_file = '/example/licenses/path/vampir.license' - modextravars = { 'VAMPIR_LICENSE': license_file, } -- GitLab From 3e51f5f2725cff3862c1ba285f7f3a1ac14d4a1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 15:17:48 +0200 Subject: [PATCH 822/992] fix bioconductor extension versions in R 3.1.3 easyconfigs --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 4 ++-- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index dee61f1e01..b43dc45c25 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -224,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.3', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 56604be04c..2863ba62ad 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -224,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.3', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), -- GitLab From c76815515fe01591e6d4e2da417e6f39ec2b806c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 15:59:48 +0200 Subject: [PATCH 823/992] {bio}[intel/2015a] BLAST+ 2.2.31 --- ...BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..e09b9fd298 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.2.31' +versionsuffix = '-Python-2.7.10' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = [ + '%(name)s-2.2.30_ictce-fixes.patch', + '%(name)s-2.2.30_basename-fixes.patch' +] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From f3470631eee344a40a8b0269574075d4755e585e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jun 2015 18:57:14 +0200 Subject: [PATCH 824/992] bump BiocInstaller version to 1.16.5 (yes, again) --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index b43dc45c25..9a8b027e4b 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.3', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 2863ba62ad..8a552002a6 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.3', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), -- GitLab From 12b514b123a5edd98c3e22ef2e63c6483331453b Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 10:10:01 +0200 Subject: [PATCH 825/992] Update CMake-3.2.3-intel-2015a.eb Add support for https --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index f4cde92c3c..749f4c4ebf 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_USE_OPENSSL=1' + dependencies = [('ncurses', '5.9')] sanity_check_paths = { -- GitLab From 0d9dd8cfab56eb2eedb6766bfdb1419a3485c434 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 10:10:49 +0200 Subject: [PATCH 826/992] Update CMake-3.2.3-foss-2015a.eb Add support for https --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb index c7935c7c64..7129af9cae 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_USE_OPENSSL=1' + dependencies = [('ncurses', '5.9')] sanity_check_paths = { -- GitLab From 186574276214d35a7b25c59c22e2690f0d31f1a9 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 11:27:05 +0200 Subject: [PATCH 827/992] Update CMake-3.2.3-intel-2015a.eb Include deps --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index 749f4c4ebf..58afb7efd9 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -14,7 +14,12 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' -dependencies = [('ncurses', '5.9')] +dependencies = [('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], -- GitLab From b7fdd6b7e840e1356693d990577140de2fb0d2cb Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 11:28:52 +0200 Subject: [PATCH 828/992] Update CMake-3.2.3-foss-2015a.eb Added necessary deps --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb index 7129af9cae..5a9f80d2eb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -14,7 +14,12 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' -dependencies = [('ncurses', '5.9')] +dependencies = [('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], -- GitLab From c48b197c3c3c17bd41d7be421c08e01ec18712e0 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Jun 2015 11:29:22 +0200 Subject: [PATCH 829/992] Update CMake-3.2.3-intel-2015a.eb typo --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index 58afb7efd9..4a3f0c85e2 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [('ncurses', '5.9'), # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], -- GitLab From 78f2b94ee1c94937ba8fa5a9c2054b475a13d3a5 Mon Sep 17 00:00:00 2001 From: npklein Date: Fri, 26 Jun 2015 22:33:46 +0200 Subject: [PATCH 830/992] samtools 1.7.20, zlib 1.27 --- .../s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb | 33 +++++++++++++++++++ .../z/zlib/zlib-1.2.7-goolf-1.7.20.eb | 22 +++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..3b814ac535 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.7'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb new file mode 100644 index 0000000000..3ae9b5cf4b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, +not covered by any patents -- lossless data-compression library for use on virtually any +computer hardware and operating system.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 509116d4d2c064b9406771f2fb3487ff25d86a99 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Jun 2015 14:15:27 +0200 Subject: [PATCH 831/992] new gcc versions --- easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb | 35 +++++++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb | 40 ++++++++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb new file mode 100644 index 0000000000..750c48766b --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -0,0 +1,35 @@ +name = "GCC" +version = '4.8.5' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.1.3.tar.bz2', + 'mpfr-3.1.2.tar.gz', + 'mpc-1.0.1.tar.gz', +] + +checksums = [ + '0c92ac45af5b280e301ca56b40fdaea2', # gcc-4.8.4.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb new file mode 100644 index 0000000000..17d5d36aba --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -0,0 +1,40 @@ +name = "GCC" +version = '4.9.3' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' -- GitLab From 6628d36b6c33edb7401ba29a0d906238d92eada5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Jun 2015 14:21:01 +0200 Subject: [PATCH 832/992] fix checksum GCC-4.8.5 --- easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb index 750c48766b..8618661532 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -21,7 +21,7 @@ sources = [ ] checksums = [ - '0c92ac45af5b280e301ca56b40fdaea2', # gcc-4.8.4.tar.gz + 'bfe56e74d31d25009c8fb55fd3ca7e01', # gcc-4.8.5.tar.gz 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz -- GitLab From a0d9b67b4bc1468d2b41e6a9e980aa100e6c89f2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Jun 2015 14:22:12 +0200 Subject: [PATCH 833/992] checksum update for GCC-4.9.3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb index 17d5d36aba..e9b0c252f8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -22,14 +22,14 @@ sources = [ 'mpc-1.0.2.tar.gz', ] -patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] checksums = [ - '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + '6f831b4d251872736e8e9cc09746f327', # gcc-4.9.3.tar.bz2 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz - '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20140630.patch ] languages = ['c', 'c++', 'fortran'] -- GitLab From 7346061a978c8ed33505f60e2764ea0b85738b17 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Jun 2015 15:43:19 +0200 Subject: [PATCH 834/992] Fix comment in GCC-4.9.3.eb --- easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb index e9b0c252f8..759f134bcc 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -29,7 +29,7 @@ checksums = [ 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz - '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20140630.patch + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch ] languages = ['c', 'c++', 'fortran'] -- GitLab From 7fc3c1381e9f7021fa9b7243f58360b848f675e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Jun 2015 13:13:25 +0200 Subject: [PATCH 835/992] {tools}[dummy] GC3Pie 2.3 --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 109 +++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb new file mode 100644 index 0000000000..796b3ed6d7 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -0,0 +1,109 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.3' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/gc3utils', 'lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg' % {'pyver': pyver}], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From 5186f8794404ad07f22fe97799db922c09b13227 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Jun 2015 15:09:02 +0200 Subject: [PATCH 836/992] enhance sanity check to also consider lib64 --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 796b3ed6d7..6fee6c35e8 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -99,8 +99,10 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', 'lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg' % {'pyver': pyver}], + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } -- GitLab From 26bb656fd47cbd8572b1c796ea92e2d83927f82b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Jun 2015 16:09:59 +0200 Subject: [PATCH 837/992] fix remarks --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 3 +-- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 9a8b027e4b..d82c3b8db2 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -47,7 +47,7 @@ bioconductor_options = { } # !! order of packages is important !! -# packages updated on January 8th 2015 +# packages updated on January 8th 2015 (last change for Bioconductor: June 25th 2015) exts_list = [ # default libraries, only here to sanity check their presence 'base', @@ -389,4 +389,3 @@ exts_list = [ ] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 8a552002a6..53bd4b0751 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -47,7 +47,7 @@ bioconductor_options = { } # !! order of packages is important !! -# packages updated on January 8th 2015 +# packages updated on January 8th 2015 (last change for Bioconductor: June 25th 2015) exts_list = [ # default libraries, only here to sanity check their presence 'base', -- GitLab From 68f5cd3c5c07cfe148b3818a02801c6941d3d7b4 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 29 Jun 2015 16:27:02 +0200 Subject: [PATCH 838/992] Add snappy support and refer Hadoop to the snappy library. This depends on a forthcoming easyblock update to support 'extra_native_libs' configuration setting in the Hadoop EasyBlock. --- .../h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 3 +++ .../s/snappy/snappy-1.1.2-intel-2015a.eb | 22 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index fea9291ff7..3fee82734e 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -19,12 +19,15 @@ builddependencies = [ ('Maven', '3.2.3'), ('protobuf', '2.5.0'), ('CMake', '3.1.3'), + ('snappy', '1.1.2'), ] dependencies = [(java, javaver)] build_native_libs = True +extra_native_libs = [(snappy, 'lib/libsnappy.so')] + parallel = 1 moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb new file mode 100644 index 0000000000..a37dfd402f --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'snappy' +version = '1.1.2' + +homepage = 'http://code.google.com/p/snappy/' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://code.google.com/p/snappy/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libsnappy.so'], + 'dirs': ['include', 'lib', 'share'] +} + +moduleclass = 'lib' + -- GitLab From 8b01fad03cb4feb97a2d4c7a0a5ea87ce53a9872 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 29 Jun 2015 16:50:21 +0200 Subject: [PATCH 839/992] Add comments based on @boegel's comments. --- easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb index a37dfd402f..e0cf7edd4c 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb @@ -15,8 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { 'files': ['lib/libsnappy.so'], - 'dirs': ['include', 'lib', 'share'] + 'dirs': ['include', 'share'] } moduleclass = 'lib' - -- GitLab From 868c8dedcac263c28882505ea38ead6551b854f6 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Mon, 29 Jun 2015 17:18:30 +0200 Subject: [PATCH 840/992] zlib 1.2.8 --- easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb index 3b814ac535..695f8c6b45 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb @@ -25,7 +25,7 @@ patches = ['SAMtools-1.1_Makefile.patch'] dependencies = [ ('ncurses', '5.9'), - ('zlib', '1.2.7'), + ('zlib', '1.2.8'), ] parallel = 1 -- GitLab From a414a99b1855a0fbf55a7f7b91cd144f35602253 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 30 Jun 2015 10:35:36 +0200 Subject: [PATCH 841/992] Snappy in quotes. --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index 3fee82734e..596ca9c73c 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -26,7 +26,7 @@ dependencies = [(java, javaver)] build_native_libs = True -extra_native_libs = [(snappy, 'lib/libsnappy.so')] +extra_native_libs = [('snappy', 'lib/libsnappy.so')] parallel = 1 -- GitLab From e456ff1e2440887f6b45f5d7d350b575e115d4c6 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 30 Jun 2015 11:55:17 +0200 Subject: [PATCH 842/992] Point eb at github for snappy (w/ the appropriate commit id for the 1.1.2 release) --- easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb index e0cf7edd4c..2a1ececd20 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'snappy' version = '1.1.2' +commit = '1ff9be9' homepage = 'http://code.google.com/p/snappy/' description = """Snappy is a compression/decompression library. It does not aim @@ -10,8 +11,8 @@ instead, it aims for very high speeds and reasonable compression.""" toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://code.google.com/p/snappy/'] -sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/google/snappy/archive'] +sources = ['%s.tar.gz' % commit] sanity_check_paths = { 'files': ['lib/libsnappy.so'], -- GitLab From 7b476311f62b3081ffddc85c9d1d295ae5a364a5 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 30 Jun 2015 12:13:51 +0200 Subject: [PATCH 843/992] Add the snappy toolchain for the Hadoop build dep. --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index 596ca9c73c..f3a7586e47 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -19,7 +19,7 @@ builddependencies = [ ('Maven', '3.2.3'), ('protobuf', '2.5.0'), ('CMake', '3.1.3'), - ('snappy', '1.1.2'), + ('snappy', '1.1.2', '-intel-2015a'), ] dependencies = [(java, javaver)] -- GitLab From e42a6186b47053238cd92af80fc93a6a502eb8be Mon Sep 17 00:00:00 2001 From: mmterpstra Date: Wed, 1 Jul 2015 14:24:06 +0200 Subject: [PATCH 844/992] Update cramtools-2.0-Java-1.7.0_80.eb - replaced tabs - removed hard coding in 'modloadmsg' - 'modloadmsg' now declared with single qoutes --- .../easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb index 19162420ed..928b078aac 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -19,11 +19,11 @@ javaver = '1.7.0_80' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -modloadmsg = """To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/cramtools-2.0.jar""" +modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" sanity_check_paths = { - 'files': ["%(name)s-%(version)s.jar"], - 'dirs': ["lib"] + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': ["lib"] } moduleclass = 'bio' -- GitLab From 6e0f7259e7cce774de924cfc823d795ea26dbe9b Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 1 Jul 2015 14:04:39 +0200 Subject: [PATCH 845/992] Add preconfigopts to run autogen.sh. Add comment explaining commit id. --- easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb index 2a1ececd20..8e40df0537 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb @@ -2,6 +2,10 @@ easyblock = 'ConfigureMake' name = 'snappy' version = '1.1.2' + +# snappy was migrated from code.google.com to github.com and this commit +# corresponds to release 1.1.2 (which they haven't tagged). +# see https://github.com/google/snappy/commit/1ff9be9 commit = '1ff9be9' homepage = 'http://code.google.com/p/snappy/' @@ -14,6 +18,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['https://github.com/google/snappy/archive'] sources = ['%s.tar.gz' % commit] +preconfigopts = "./autogen.sh && " + sanity_check_paths = { 'files': ['lib/libsnappy.so'], 'dirs': ['include', 'share'] -- GitLab From 512a73efaa6900a8beeee17612f223a4e87edc0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jul 2015 17:47:18 +0200 Subject: [PATCH 846/992] rename R bundles so they don't conflict on each other --- .../R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb} | 6 +++--- .../R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb} | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/r/{R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb => R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb} (91%) rename easybuild/easyconfigs/r/{R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb => R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb} (98%) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb similarity index 91% rename from easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb rename to easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb index 5a2b464944..c20e9fab18 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb @@ -1,9 +1,9 @@ easyblock = 'Bundle' -name = 'R-bundle' +name = 'R-bundle-devtools' version = '20150520' rver = '3.1.3' -versionsuffix = '-R-%s-devtools' % rver +versionsuffix = '-R-%s' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -16,7 +16,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('R-bundle', '20150323', '-R-%s-extra' % rver), + ('R-bundle-extra', '20150323', '-R-%s' % rver), ] ext_options = { diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb similarity index 98% rename from easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb rename to easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb index a6d53af385..96c79b8200 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb @@ -1,9 +1,9 @@ easyblock = 'Bundle' -name = 'R-bundle' +name = 'R-bundle-extra' version = '20150323' rver = '3.1.3' -versionsuffix = '-R-%s-extra' % rver +versionsuffix = '-R-%s' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" -- GitLab From ebebd211cf5b2506febd6bbfb7ad2cc9499ab818 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jul 2015 13:52:37 +0200 Subject: [PATCH 847/992] {chem}[intel/2015a] CP2K 20130228 --- .../b/Bison/Bison-2.7-intel-2015a.eb | 22 ++++++++++++ .../c/CP2K/CP2K-20130228-intel-2015a.eb | 36 +++++++++++++++++++ .../f/FFTW/FFTW-3.3.3-intel-2015a.eb | 34 ++++++++++++++++++ .../f/flex/flex-2.5.37-intel-2015a.eb | 14 ++++++++ 4 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb new file mode 100644 index 0000000000..48aa608e0d --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb new file mode 100644 index 0000000000..fd8d96a13d --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb @@ -0,0 +1,36 @@ +name = 'CP2K' +version = '20130228' + +homepage = 'http://cp2k.berlios.de/index.html' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular +simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different +methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and +classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = ['CP2K-%(version)s.tar.gz'] + +patches = [ + 'CP2K-2013_fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch', +] + +dependencies = [ + ('FFTW', '3.3.3'), + ('Libint', '1.1.4'), +] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb new file mode 100644 index 0000000000..10fd990805 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.3' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +# see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb new file mode 100644 index 0000000000..086db50be8 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' -- GitLab From a831b17749160a27620eaa69ffdd267e0ec65d58 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jul 2015 14:21:35 +0200 Subject: [PATCH 848/992] add missing patch file --- .../c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch new file mode 100644 index 0000000000..7533a55308 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch @@ -0,0 +1,11 @@ +--- cp2k/makefiles/Makefile.orig 2013-02-04 17:55:57.000000000 +0100 ++++ cp2k/makefiles/Makefile 2013-02-05 17:55:06.811020304 +0100 +@@ -200,7 +200,7 @@ + # + ifeq ($(CPPSHELL),) + CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ +- -D__COMPILE_DATE="\"$(shell date)\""\ ++ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g'))\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ + -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" + endif -- GitLab From 4e756528393d07d55a277f94e495eb10d6849fbf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jul 2015 16:34:01 +0200 Subject: [PATCH 849/992] include custom sanity_check_paths for R bundles --- .../R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb | 6 +++++- .../R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb | 5 +++++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb index c20e9fab18..aa48ed3b81 100644 --- a/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb @@ -41,5 +41,9 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} -moduleclass = 'lang' +sanity_check_paths = { + 'files': [], + 'dirs': ['devtools'], +} +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb index 96c79b8200..1bde4e9f5d 100644 --- a/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb @@ -92,4 +92,9 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} +sanity_check_paths = { + 'files': [], + 'dirs': ['RCurl', 'XML', 'spliceR'], +} + moduleclass = 'lang' -- GitLab From b0b333fee30fc82e8260523f70695450acc57b42 Mon Sep 17 00:00:00 2001 From: Caroline De Brouwer Date: Thu, 2 Jul 2015 16:38:32 +0200 Subject: [PATCH 850/992] Test dump method on every easyconfig file --- test/easyconfigs/easyconfigs.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 838f4a2957..c9c6efcdfe 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -52,6 +52,7 @@ from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool from easybuild.tools.robot import resolve_dependencies +from easybuild.tools.filetools import read_file, write_file # indicates whether all the single tests are OK, @@ -235,7 +236,9 @@ def template_easyconfig_test(self, spec): prev_single_tests_ok = single_tests_ok single_tests_ok = False - # parse easyconfig + ec_orig = read_file(spec) + + # parse easyconfig ecs = process_easyconfig(spec) if len(ecs) == 1: ec = ecs[0]['ec'] @@ -250,7 +253,7 @@ def template_easyconfig_test(self, spec): name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) # sanity check for software name - self.assertTrue(ec['name'], name) + self.assertTrue(ec['name'], name) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) @@ -297,6 +300,14 @@ def template_easyconfig_test(self, spec): app.close_log() os.remove(app.logfile) + # dump the easyconfig file + ec.dump('test.eb') + dumped_ec = EasyConfig('test.eb') + + self.assertEqual(ec['name'], dumped_ec['name']) + self.assertEqual(ec['version'], dumped_ec['version']) + self.assertEqual(ec['sanity_check_paths'], dumped_ec['sanity_check_paths']) + # cache the parsed easyconfig, to avoid that it is parsed again self.parsed_easyconfigs.append(ecs[0]) -- GitLab From adb1f38506c7af0ca7c38c06654c05e0d3afd09a Mon Sep 17 00:00:00 2001 From: Caroline De Brouwer Date: Thu, 2 Jul 2015 16:51:12 +0200 Subject: [PATCH 851/992] remove unnecessary lines --- test/easyconfigs/easyconfigs.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c9c6efcdfe..744dbffc53 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -52,8 +52,6 @@ from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool from easybuild.tools.robot import resolve_dependencies -from easybuild.tools.filetools import read_file, write_file - # indicates whether all the single tests are OK, # and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well @@ -236,8 +234,6 @@ def template_easyconfig_test(self, spec): prev_single_tests_ok = single_tests_ok single_tests_ok = False - ec_orig = read_file(spec) - # parse easyconfig ecs = process_easyconfig(spec) if len(ecs) == 1: -- GitLab From 8d5e1eeaf6c0bf445ee150d4cf0dda78bba47c82 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 2 Jul 2015 17:04:47 +0200 Subject: [PATCH 852/992] Use only GCC (no toolchain) and use 4th arg for build dep. --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 2 +- .../{snappy-1.1.2-intel-2015a.eb => snappy-1.1.2-GCC-4.9.2.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/snappy/{snappy-1.1.2-intel-2015a.eb => snappy-1.1.2-GCC-4.9.2.eb} (94%) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index f3a7586e47..e94d4f7d23 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -19,7 +19,7 @@ builddependencies = [ ('Maven', '3.2.3'), ('protobuf', '2.5.0'), ('CMake', '3.1.3'), - ('snappy', '1.1.2', '-intel-2015a'), + ('snappy', '1.1.2', '', ('GCC', '4.9.2')), ] dependencies = [(java, javaver)] diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb similarity index 94% rename from easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb rename to easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb index 8e40df0537..551924427d 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb @@ -13,7 +13,7 @@ description = """Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['https://github.com/google/snappy/archive'] sources = ['%s.tar.gz' % commit] -- GitLab From c5f9c342a1b75d17942001c136d66b1a04215385 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 09:59:10 +0200 Subject: [PATCH 853/992] {lib}[intel/2015a] gensim 0.11.1-1 --- ...nsim-0.11.1-1-intel-2015a-Python-2.7.10.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..f497f88541 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'gensim' +version = '0.11.1-1' + +homepage = 'https://pypi.python.org/pypi/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +moduleclass = 'lib' -- GitLab From 5f1cc312d0ce41468705551027478b840742f757 Mon Sep 17 00:00:00 2001 From: Caroline De Brouwer Date: Fri, 3 Jul 2015 10:18:46 +0200 Subject: [PATCH 854/992] dump test full config --- test.eb | 19 +++++++++++++++++++ test/easyconfigs/easyconfigs.py | 14 +++++++++----- 2 files changed, 28 insertions(+), 5 deletions(-) create mode 100644 test.eb diff --git a/test.eb b/test.eb new file mode 100644 index 0000000000..0e62d9dea1 --- /dev/null +++ b/test.eb @@ -0,0 +1,19 @@ +easyblock = "Tarball" + +name = "ABINIT" +version = "7.0.3" +versionsuffix = "-x86_64_linux_gnu4.5" + +homepage = "http://www.abinit.org/" +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = [('abinit-7.0.3_x86_64_linux_gnu4.5.bz2', 'tar xfj %s')] +source_urls = ['http://ftp.abinit.org/'] + + +sanity_check_paths = {'files': ['bin/abinit'], 'dirs': []} + +moduleclass = "chem" \ No newline at end of file diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 744dbffc53..bba0b94318 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -53,6 +53,7 @@ from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool from easybuild.tools.robot import resolve_dependencies + # indicates whether all the single tests are OK, # and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well # other than optimizing for time, this also helps to get around problems like http://bugs.python.org/issue10949 @@ -297,12 +298,15 @@ def template_easyconfig_test(self, spec): os.remove(app.logfile) # dump the easyconfig file - ec.dump('test.eb') - dumped_ec = EasyConfig('test.eb') + handle, test_ecfile = tempfile.mkstemp() + os.close(handle) + + ec.dump(test_ecfile) + dumped_ec = EasyConfig(test_ecfile) + os.remove(test_ecfile) - self.assertEqual(ec['name'], dumped_ec['name']) - self.assertEqual(ec['version'], dumped_ec['version']) - self.assertEqual(ec['sanity_check_paths'], dumped_ec['sanity_check_paths']) + for key in sorted(ec._config): + self.assertEqual(ec[key], dumped_ec[key]) # cache the parsed easyconfig, to avoid that it is parsed again self.parsed_easyconfigs.append(ecs[0]) -- GitLab From 656407932c9d4c7cd4439366a95c35e45a9a75c1 Mon Sep 17 00:00:00 2001 From: Caroline De Brouwer Date: Fri, 3 Jul 2015 10:19:31 +0200 Subject: [PATCH 855/992] Delete test.eb --- test.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 test.eb diff --git a/test.eb b/test.eb deleted file mode 100644 index 0e62d9dea1..0000000000 --- a/test.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = "Tarball" - -name = "ABINIT" -version = "7.0.3" -versionsuffix = "-x86_64_linux_gnu4.5" - -homepage = "http://www.abinit.org/" -description = """Abinit is a plane wave pseudopotential code for doing - condensed phase electronic structure calculations using DFT.""" - -toolchain = {'version': 'dummy', 'name': 'dummy'} - -sources = [('abinit-7.0.3_x86_64_linux_gnu4.5.bz2', 'tar xfj %s')] -source_urls = ['http://ftp.abinit.org/'] - - -sanity_check_paths = {'files': ['bin/abinit'], 'dirs': []} - -moduleclass = "chem" \ No newline at end of file -- GitLab From a331bbc485af537c090dab17f425bb59bb5a7ef3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 3 Jul 2015 10:51:32 +0200 Subject: [PATCH 856/992] seaborn easyconfig --- ...Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..63cb8346de --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'Seaborn' +version = '0.6.0' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/mwaskom/seaborn/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'bio' -- GitLab From 7cfbf96ed8bb6afc4b64c6ad1d4379a4cdba62e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 14:45:25 +0200 Subject: [PATCH 857/992] remove exts_filter definition from Python 3.4.3 easyconfig, as it can cause problems --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index a71f6ecf62..1aa8ae3172 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -27,7 +27,6 @@ osdependencies = [('openssl-devel', 'libssl-dev')] # order is important! # package versions updated Jan 19th 2015 -exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') exts_list = [ ('setuptools', '15.2', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], -- GitLab From cfbc6e966d0e64f230d17267a2d2acf8a55a7554 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 18:18:14 +0200 Subject: [PATCH 858/992] style fixes in NEMO easyconfig --- easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb index cc73946e3e..a4b50a7074 100644 --- a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb @@ -2,14 +2,18 @@ name = 'NEMO' version = '3.4' homepage = 'http://www.nemo-ocean.eu/' -description = 'NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for oceanographic research, operational oceanography seasonal forecast and climate studies.' +description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for + oceanographic research, operational oceanography seasonal forecast and climate studies.""" toolchain = {'name': 'ictce','version': '6.1.5'} toolchainopts = {'opt': False, 'optarch': False} +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('netCDF-Fortran', '4.2')] + with_components = ['OPA_SRC', 'LIM_SRC_3'] add_keys = ['key_iomput', 'key_mpp_mpi', 'key_dtasal', 'key_dtatem', 'key_tradmp', 'key_lim3', 'key_orca_r1=75'] del_keys = ['key_lim2', 'key_zdftmx', 'key_orca_r2'] -sources = [SOURCELOWER_TAR_GZ] -dependencies = [('netCDF-Fortran', '4.2')] +moduleclass = 'geo' -- GitLab From 2bfb7fd19de8a7fe899f27325032b04071c637bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 18:22:50 +0200 Subject: [PATCH 859/992] include SVN revision in version, add instructions on obtaining sources --- ...MO-3.4-ictce-6.1.5.eb => NEMO-3.4-r5541-ictce-6.1.5.eb} | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/NEMO/{NEMO-3.4-ictce-6.1.5.eb => NEMO-3.4-r5541-ictce-6.1.5.eb} (72%) diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb similarity index 72% rename from easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb rename to easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb index a4b50a7074..27572d3f2a 100644 --- a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb @@ -1,5 +1,5 @@ name = 'NEMO' -version = '3.4' +version = '3.4-r5541' homepage = 'http://www.nemo-ocean.eu/' description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for @@ -8,7 +8,10 @@ description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-o toolchain = {'name': 'ictce','version': '6.1.5'} toolchainopts = {'opt': False, 'optarch': False} -sources = [SOURCELOWER_TAR_GZ] +# authenticated SVN access required +# svn --username 'login' co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2012/dev_v3_4_STABLE_2012 +# tar cfvz NEMO-3.4-r.tar.gz dev_v3_4_STABLE_2012 +sources = [SOURCE_TAR_GZ] dependencies = [('netCDF-Fortran', '4.2')] -- GitLab From 0b52721d54adb12815e6e436ec83bd25fc2f9194 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 18:28:24 +0200 Subject: [PATCH 860/992] add missing easyconfigs for (indirect) NEMO dependencies --- .../b/Bison/Bison-2.7-ictce-6.1.5.eb | 22 +++++++++++++++ .../d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb | 18 +++++++++++++ .../f/flex/flex-2.5.37-ictce-6.1.5.eb | 14 ++++++++++ .../h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb | 27 +++++++++++++++++++ .../easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb | 26 ++++++++++++++++++ .../netCDF-Fortran-4.2-ictce-6.1.5.eb | 18 +++++++++++++ .../n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb | 19 +++++++++++++ .../s/Szip/Szip-2.1-ictce-6.1.5.eb | 23 ++++++++++++++++ .../z/zlib/zlib-1.2.7-ictce-6.1.5.eb | 22 +++++++++++++++ 9 files changed, 189 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb new file mode 100644 index 0000000000..deba4d2a79 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.16')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb new file mode 100644 index 0000000000..2f5d07d58f --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb new file mode 100644 index 0000000000..15e30d50fb --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb new file mode 100644 index 0000000000..caf75ce765 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management + of extremely large and complex data collections.""" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb new file mode 100644 index 0000000000..062e490de1 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.16' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + + +toolchain = {'name': 'ictce', 'version': '6.1.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['M4-%(version)s-no-gets.patch'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb new file mode 100644 index 0000000000..87478cf832 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.2.1.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb new file mode 100644 index 0000000000..262ebc70b9 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb @@ -0,0 +1,19 @@ +name = 'netCDF' +version = '4.2.1.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('HDF5', '1.8.10', '-gpfs')] + +builddependencies = [('Doxygen', '1.8.3.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb new file mode 100644 index 0000000000..d90d48702e --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb new file mode 100644 index 0000000000..62b9777b1c --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From cf1d950b8751b5ad91981c1a8c87c6cc70ba5884 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 20:31:54 +0200 Subject: [PATCH 861/992] fix source_urls in netCDF easyconfigs --- .../n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb | 5 ++++- .../n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb | 5 ++++- .../n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb | 5 ++++- .../n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb | 12 +++++++----- .../n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb | 5 ++++- .../n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb | 12 +++++++----- .../n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb | 5 ++++- .../netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-intel-2014b.eb | 5 ++++- .../n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb | 5 ++++- .../easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb | 5 ++++- 23 files changed, 98 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb index e83acc3cca..aaee694b4f 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb index 8bf5c28625..6aa937d650 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb index c00c295552..3d4e4b8034 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb index 4a0335f764..1cf87a93d6 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb index eef9aa4fe1..2e121dba81 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb @@ -6,16 +6,18 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ - ('HDF5', '1.8.9'), - ('Doxygen', '1.8.1.1') - ] + ('HDF5', '1.8.9'), + ('Doxygen', '1.8.1.1'), +] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb index 827d6154da..8a0164a41a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb index 3f8634ce66..9278dcabb7 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb index 738b574b64..70579f3686 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb index b51011ebf8..bf3bcad88f 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb @@ -6,16 +6,18 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ - ('HDF5', '1.8.9'), - ('Doxygen', '1.8.1.1') - ] + ('HDF5', '1.8.9'), + ('Doxygen', '1.8.1.1'), +] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb index 4f975041bc..8ae8d0db4f 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb index a8fa0bc40a..4527973704 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb index 1d208f1301..a518b2a451 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb @@ -11,7 +11,10 @@ toolchain = {'name':'ictce','version':'4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs-mt')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb index a43794119f..9caf198302 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name':'ictce','version':'4.1.13'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb index 5c53c8bf57..081ab64f4b 100755 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.10', '-gpfs%(versionsuffix)s'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb index b2e2392049..59a30799c7 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb index 5e5d78307e..a238c0cf33 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb index fa034d1498..69ddb9f9ca 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb index dd168910be..741f74cd63 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb index 78d6d431c3..a3bce6fa83 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [('netCDF-4.3.0_nc-config.in.cmake', 'netcdf-4.3.0')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb index ffb64828a3..f0b637b12c 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [ 'netCDF-4.3.2-with-HDF-1.8.13.patch', diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb index e42de69332..d7b013c418 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [ 'netCDF-4.3.2-with-HDF-1.8.13.patch', diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb index 172783a9aa..e848a71eec 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [ 'netCDF-4.3.2-with-HDF-1.8.13.patch', diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb index 0456d513c3..623ceccdb3 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [ 'netCDF-4.3.2-with-HDF-1.8.13.patch', -- GitLab From 2699d9477fa0ccaacc963980f33a7f9bbcb7403d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jul 2015 20:41:48 +0200 Subject: [PATCH 862/992] fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs --- .../easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb | 5 ++++- .../n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb | 5 ++++- .../easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb | 5 ++++- .../easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb | 5 ++++- .../easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb | 5 ++++- .../netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb | 6 +++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb | 6 ++++-- .../n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb | 6 ++++-- .../n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb | 5 ++++- .../n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb | 6 ++++-- .../n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb | 5 ++++- 17 files changed, 69 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb index b46d95de45..e0cfb1558e 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb index 57f1d3e4bb..d47cb17c75 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb @@ -13,7 +13,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('netCDF', '4.2.1.1', versionsuffix), diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb index 7a7c4b81bc..400224b911 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb index 3b4f3e5332..16ea5317c4 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb index de008bf235..d8cdaf41c4 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb index 091c9e9f89..adc9cf91dc 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', version)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb index f4a44d81d3..2caeeaf083 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb @@ -5,11 +5,15 @@ homepage = 'http://www.unidata.ucar.edu/software/netcdf/' description = """NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb index a8cbfe5ddb..bd158f66c5 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb index fac88a30ba..d4ddc1b2b5 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', version)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb index 6b36f2c00b..b50fb138ef 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1', versionsuffix)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb index ef015a9175..40fd553f1f 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb index 4686402139..09084630c1 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb index b0bef7e67a..f7f72fcd32 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb index 4d00f104ad..c51e1a7941 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb index d623122642..9b2aa29afe 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb index 59ed0da09a..7823a5fa7d 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb index ed31b043f1..39adb73d6e 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] -- GitLab From dc66e3f090c96e10fbdcd51f477c5afa1fc8cf7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jul 2015 11:01:49 +0200 Subject: [PATCH 863/992] {tools}[dummy] GC3Pie 2.4.0 --- .../easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb new file mode 100644 index 0000000000..8a1d9386f8 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.0' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From affa6314feea3d9c3c71163a58f072edb5d1c282 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 11:09:34 +0300 Subject: [PATCH 864/992] Contributing Biggus Python Package --- ...Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb | 22 +++++++++++++++++++ .../Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..46e8bcb1a8 --- /dev/null +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,22 @@ +easyblock = "PythonPackage" + +name = 'Biggus' +version = '0.11.0' + +homepage = 'https://github.com/SciTools/biggus' +description = """Virtual large arrays and lazy evaluation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..4374be186c --- /dev/null +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,22 @@ +easyblock = "PythonPackage" + +name = 'Biggus' +version = '0.5.0' + +homepage = 'https://github.com/SciTools/biggus' +description = """Virtual large arrays and lazy evaluation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +moduleclass = 'data' -- GitLab From f8984993b96be359549b82b1029abc6363621590 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 12:42:09 +0300 Subject: [PATCH 865/992] Contributing BSMAP --- .../b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb | 35 +++++++++ easybuild/easyconfigs/b/BSMAP/makefile.patch | 19 +++++ easybuild/easyconfigs/b/BSMAP/param.patch | 7 ++ easybuild/easyconfigs/b/BSMAP/samtools.patch | 76 +++++++++++++++++++ 4 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/BSMAP/makefile.patch create mode 100644 easybuild/easyconfigs/b/BSMAP/param.patch create mode 100644 easybuild/easyconfigs/b/BSMAP/samtools.patch diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb new file mode 100644 index 0000000000..51f6971d10 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'BSMAP' +version = '2.74' + +homepage = 'https://code.google.com/p/bsmap/' +description = """BSMAP is a short reads mapping software for bisulfite sequencing reads.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://bsmap.googlecode.com/files/'] +sources = [SOURCELOWER_TGZ] + +skipsteps = ['configure'] + +installopts = "INSTALL_DIR=%(installdir)s" + +patches = [ + 'makefile.patch', + 'param.patch', + 'samtools.patch', +] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.7'), + ('SAMtools', '0.1.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bsmap", "methratio.py", "sam2bam.sh"]], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BSMAP/makefile.patch b/easybuild/easyconfigs/b/BSMAP/makefile.patch new file mode 100644 index 0000000000..f015ee9ecd --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/makefile.patch @@ -0,0 +1,19 @@ +--- bsmap-2.74/makefile.orig 2012-09-20 23:01:57.000000000 +0300 ++++ bsmap-2.74/makefile 2014-12-16 09:24:16.033631393 +0200 +@@ -1,6 +1,6 @@ + CC= g++ + +-BIN = $(DESTDIR)/usr/bin ++BIN=$(INSTALL_DIR)/bin + FLAGS= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 + #FLAGS= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -Wall -Wno-strict-aliasing -m64 + +@@ -16,7 +16,7 @@ + bsmap: $(OBJS1) + (cd samtools; make) + (cd gzstream; make) +- $(CC) $(FLAGS) $^ -o $@ $(THREAD) -lbam -lz -lgzstream ++ $(CC) $(FLAGS) $^ -o $@ $(THREAD) -lbam -L$(EBROOTZLIB)/lib -lz -lgzstream + rm -f *.o + + clean: diff --git a/easybuild/easyconfigs/b/BSMAP/param.patch b/easybuild/easyconfigs/b/BSMAP/param.patch new file mode 100644 index 0000000000..8c645688c9 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/param.patch @@ -0,0 +1,7 @@ +--- param.cpp.orig 2014-12-08 22:13:01.439639000 +0200 ++++ param.cpp 2014-12-08 22:14:20.305028000 +0200 +@@ -1,3 +1,4 @@ ++#include + #include "param.h" + #include + diff --git a/easybuild/easyconfigs/b/BSMAP/samtools.patch b/easybuild/easyconfigs/b/BSMAP/samtools.patch new file mode 100644 index 0000000000..714b79ef91 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/samtools.patch @@ -0,0 +1,76 @@ +--- bsmap-2.74/samtools/Makefile.orig 2014-12-15 14:42:22.628493847 +0200 ++++ bsmap-2.74/samtools/Makefile 2014-12-15 14:42:51.729602124 +0200 +@@ -10,10 +10,11 @@ + bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \ + cut_target.o phase.o bam2depth.o + PROG= samtools +-INCLUDES= -I. ++INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I. + SUBDIRS= . bcftools misc +-LIBPATH= +-#LIBCURSES= -lcurses # -lXCurses ++LIBPATH= -L$(EBROOTZLIB)/lib ++LIBCURSES= -L$(EBROOTNCURSES)/lib -lcurses -L$(EBROOTZLIB)/lib -lz # -lXCurses ++ + + .SUFFIXES:.c .o + +@@ -44,10 +45,10 @@ + $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz + + razip:razip.o razf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz ++ $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -L$(EBROOTZLIB)/lib -lz + + bgzip:bgzip.o bgzf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz ++ $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -L$(EBROOTZLIB)/lib -lz + + razip.o:razf.h + bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h +@@ -73,10 +74,10 @@ + + + libbam.1.dylib-local:$(LOBJS) +- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz ++ libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -L$(EBROOTZLIB)/lib -lz + + libbam.so.1-local:$(LOBJS) +- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz ++ $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -L$(EBROOTZLIB)/lib -lz + + dylib: + @$(MAKE) cleanlocal; \ +--- bsmap-2.74/samtools/misc/Makefile.orig 2012-09-20 23:01:58.000000000 +0300 ++++ bsmap-2.74/samtools/misc/Makefile 2014-12-15 14:40:50.817493925 +0200 +@@ -28,13 +28,13 @@ + lib: + + seqtk:seqtk.o +- $(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ seqtk.o -lm -L$(EBROOTZLIB)/lib -lz + + wgsim:wgsim.o +- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ wgsim.o -lm -L$(EBROOTZLIB)/lib -lz + + md5fa:md5.o md5fa.o md5.h ../kseq.h +- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz ++ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -L$(EBROOTZLIB)/lib -lz + + md5sum-lite:md5sum-lite.o + $(CC) $(CFLAGS) -o $@ md5sum-lite.o +@@ -43,10 +43,10 @@ + $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c + + maq2sam-short:maq2sam.c +- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz +- ++ $(CC) $(CFLAGS) -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz ++ + maq2sam-long:maq2sam.c +- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz + + md5fa.o:md5.h md5fa.c + $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c -- GitLab From fe4db4b4391463e47a4ac55d4c89955fc3bec529 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jul 2015 11:47:52 +0200 Subject: [PATCH 866/992] include URL with info on supported keys, sort alphabetically --- easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb index 27572d3f2a..fd8734e64f 100644 --- a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb @@ -15,8 +15,9 @@ sources = [SOURCE_TAR_GZ] dependencies = [('netCDF-Fortran', '4.2')] +# see http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/cpp-keys-v3_4 with_components = ['OPA_SRC', 'LIM_SRC_3'] -add_keys = ['key_iomput', 'key_mpp_mpi', 'key_dtasal', 'key_dtatem', 'key_tradmp', 'key_lim3', 'key_orca_r1=75'] -del_keys = ['key_lim2', 'key_zdftmx', 'key_orca_r2'] +add_keys = ['key_dtasal', 'key_dtatem', 'key_lim3', 'key_iomput', 'key_mpp_mpi', 'key_orca_r1=75', 'key_tradmp'] +del_keys = ['key_lim2', 'key_orca_r2', 'key_zdftmx'] moduleclass = 'geo' -- GitLab From bb9e83280daf1aa47ddf729ee80530b420693e60 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 12:53:42 +0300 Subject: [PATCH 867/992] Contributing mpi4py python package built with Python 3.2.3 --- .../mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb new file mode 100644 index 0000000000..f3694ef966 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3' + +homepage = 'https://code.google.com/p/mpi4py/' +description = """MPI for Python (mpi4py) provides bindings of the +Message Passing Interface (MPI) standard for the Python programming +language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [ + BITBUCKET_DOWNLOADS, + GOOGLECODE_SOURCE, +] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.2.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'mpi' -- GitLab From b1d8483fd7f29470bfe757f95d467d56a4cb5d1f Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 7 Jul 2015 12:22:21 +0200 Subject: [PATCH 868/992] Glob the lib so. --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index e94d4f7d23..0b189ca56d 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -26,7 +26,7 @@ dependencies = [(java, javaver)] build_native_libs = True -extra_native_libs = [('snappy', 'lib/libsnappy.so')] +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] parallel = 1 -- GitLab From bcf3bf0075d0dd1edab559f4914c5b29e12f138e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jul 2015 12:23:18 +0200 Subject: [PATCH 869/992] add IC3 versionsuffix to NEMO easyconfig, clarify add_keys/del_keys --- ...1-ictce-6.1.5.eb => NEMO-3.4-r5541-ictce-6.1.5-IC3.eb} | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/n/NEMO/{NEMO-3.4-r5541-ictce-6.1.5.eb => NEMO-3.4-r5541-ictce-6.1.5-IC3.eb} (67%) diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb similarity index 67% rename from easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb rename to easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb index fd8734e64f..3f22d89443 100644 --- a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb @@ -1,5 +1,6 @@ name = 'NEMO' version = '3.4-r5541' +versionsuffix = '-IC3' homepage = 'http://www.nemo-ocean.eu/' description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for @@ -15,8 +16,13 @@ sources = [SOURCE_TAR_GZ] dependencies = [('netCDF-Fortran', '4.2')] -# see http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/cpp-keys-v3_4 +# setting specific to IC3 +# enable ocean model and Louvain-la-Neuve sea-ice model +# see http://www.nemo-ocean.eu/About-NEMO with_components = ['OPA_SRC', 'LIM_SRC_3'] +# enable LIM3, MPI, IOM, global ORCA config at 1 degree resolution (& more) +# disable LIM2, global ORCA config at 2 degree resolution, tides induced vertical mixing +# see http://www.nemo-ocean.eu/About-NEMO, http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/cpp-keys-v3_4 add_keys = ['key_dtasal', 'key_dtatem', 'key_lim3', 'key_iomput', 'key_mpp_mpi', 'key_orca_r1=75', 'key_tradmp'] del_keys = ['key_lim2', 'key_orca_r2', 'key_zdftmx'] -- GitLab From a473b3bc317f55f0bc63566b218cbb8ceee7000f Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 14:38:31 +0300 Subject: [PATCH 870/992] Changing patch files names --- easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb | 6 +++--- .../{makefile.patch => BSMAP-2.74_makefile-modif.patch} | 3 +++ .../BSMAP/{param.patch => BSMAP-2.74_parameters-cpp.patch} | 2 ++ .../{samtools.patch => BSMAP-2.74_samtools-deps.patch} | 2 ++ 4 files changed, 10 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/b/BSMAP/{makefile.patch => BSMAP-2.74_makefile-modif.patch} (80%) rename easybuild/easyconfigs/b/BSMAP/{param.patch => BSMAP-2.74_parameters-cpp.patch} (69%) rename easybuild/easyconfigs/b/BSMAP/{samtools.patch => BSMAP-2.74_samtools-deps.patch} (96%) diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb index 51f6971d10..e7342e0349 100644 --- a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -16,9 +16,9 @@ skipsteps = ['configure'] installopts = "INSTALL_DIR=%(installdir)s" patches = [ - 'makefile.patch', - 'param.patch', - 'samtools.patch', + 'BSMAP-2.74_makefile-modif.patch', + 'BSMAP-2.74_parameters-cpp.patch', + 'BSMAP-2.74_samtools-deps.patch', ] dependencies = [ diff --git a/easybuild/easyconfigs/b/BSMAP/makefile.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch similarity index 80% rename from easybuild/easyconfigs/b/BSMAP/makefile.patch rename to easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch index f015ee9ecd..7992065109 100644 --- a/easybuild/easyconfigs/b/BSMAP/makefile.patch +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch @@ -1,3 +1,6 @@ +Patch to point to the correct bin directory in the EASYBUILDINSTALLDIR and to +the correct location of the ZLIB libraries +Thekla Loizou July 2015 --- bsmap-2.74/makefile.orig 2012-09-20 23:01:57.000000000 +0300 +++ bsmap-2.74/makefile 2014-12-16 09:24:16.033631393 +0200 @@ -1,6 +1,6 @@ diff --git a/easybuild/easyconfigs/b/BSMAP/param.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch similarity index 69% rename from easybuild/easyconfigs/b/BSMAP/param.patch rename to easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch index 8c645688c9..21007be7d3 100644 --- a/easybuild/easyconfigs/b/BSMAP/param.patch +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch @@ -1,3 +1,5 @@ +Patch to include unitstd.h in the parameters for cpp +Thekla Loizou July 2015 --- param.cpp.orig 2014-12-08 22:13:01.439639000 +0200 +++ param.cpp 2014-12-08 22:14:20.305028000 +0200 @@ -1,3 +1,4 @@ diff --git a/easybuild/easyconfigs/b/BSMAP/samtools.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch similarity index 96% rename from easybuild/easyconfigs/b/BSMAP/samtools.patch rename to easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch index 714b79ef91..7475b92e92 100644 --- a/easybuild/easyconfigs/b/BSMAP/samtools.patch +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch @@ -1,3 +1,5 @@ +Patch to point to the correct locations of SAMTools dependencies +Thekla Loizou July 2015 --- bsmap-2.74/samtools/Makefile.orig 2014-12-15 14:42:22.628493847 +0200 +++ bsmap-2.74/samtools/Makefile 2014-12-15 14:42:51.729602124 +0200 @@ -10,10 +10,11 @@ -- GitLab From e54e5fe645a618e2f859c00abb0f1a34a7acb693 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 15:13:31 +0300 Subject: [PATCH 871/992] Contributing ordereddict Python package --- ...dereddict-1.1-goolf-1.4.10-Python-2.7.3.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..5fe608081a --- /dev/null +++ b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'ordereddict' +version = '1.1' + +homepage = 'https://pypi.python.org/pypi/ordereddict' +description = """Drop-in substitute for Py2.7's new collections.OrderedDict. +The recipe has big-oh performance that matches regular dictionaries (amortized +O(1) insertion/deletion/lookup and O(n) iteration/repr/copy/equality_testing).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://pypi.python.org/packages/source/o/%s/' % name.lower()] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +sanity_check_paths = { + 'files': [], + 'dirs': ['.'], +} + +moduleclass = 'data' -- GitLab From 98ef6b15062ccb5baf74000731b4769b0146b5c7 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 15:28:30 +0300 Subject: [PATCH 872/992] Contriburing rpy2 Python Package --- .../rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb | 25 +++++++++++++++++++ .../rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..aeaed8d595 --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'rpy2' +version = '2.4.3' + +homepage = 'http://rpy.sourceforge.net/' +description = """rpy2 is a redesign and rewrite of rpy. It is providing a low-level +interface to R from Python, a proposed high-level interface, including wrappers to +graphical libraries, as well as R-like structures and functions. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('R', '2.15.2'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb new file mode 100644 index 0000000000..6d5edb8ec2 --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'rpy2' +version = '2.4.3' + +homepage = 'http://rpy.sourceforge.net/' +description = """rpy2 is a redesign and rewrite of rpy. It is providing a low-level +interface to R from Python, a proposed high-level interface, including wrappers to +graphical libraries, as well as R-like structures and functions. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.2.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('R', '2.15.2'), +] + +moduleclass = 'mpi' -- GitLab From b609405807703f4192290fc9a85a0cb2e67edfac Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 15:39:29 +0300 Subject: [PATCH 873/992] Contributing Pyke Python Package --- .../Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..2453963f18 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Pyke' +version = '1.1.1' + +homepage = 'http://sourceforge.net/projects/pyke/' +description = """Pyke introduces a form of Logic Programming (inspired by Prolog) +to the Python community by providing a knowledge-based inference engine +(expert system) written in 100% Python.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('numpy','1.6.2', versionsuffix), + ('scipy', '0.11.0', versionsuffix), +] + +moduleclass = 'data' -- GitLab From 6a574354c714fe1dcb9534050b737f94a882bb07 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Tue, 7 Jul 2015 16:06:25 +0300 Subject: [PATCH 874/992] Changes in easyconfig file --- .../ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb index 5fe608081a..a404ae249a 100644 --- a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb @@ -10,7 +10,7 @@ O(1) insertion/deletion/lookup and O(n) iteration/repr/copy/equality_testing)."" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/o/%s/' % name.lower()] +source_urls = ['http://pypi.python.org/packages/source/o/%(namelower)s'] sources = [SOURCELOWER_TAR_GZ] python = "Python" @@ -21,9 +21,4 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] -sanity_check_paths = { - 'files': [], - 'dirs': ['.'], -} - moduleclass = 'data' -- GitLab From e53a62536f35adaf79819b1aabe1a4cafc7bfddf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jul 2015 19:09:00 +0200 Subject: [PATCH 875/992] {perf}[intel/2015a] OSU Micro-Benchmarks v4.4.1 --- .../OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb new file mode 100644 index 0000000000..43857d07e3 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '4.4.1' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +configopts = 'CC="$MPICC"' + +modextrapaths = {'PATH': ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']]} + +sanity_check_paths = { + 'files': [], + 'dirs': ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']], +} + +moduleclass = 'perf' -- GitLab From afa53f5a6e78c96dc445141db44f006a28c54cce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jul 2015 21:23:19 +0200 Subject: [PATCH 876/992] fix remarks --- .../OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb index 43857d07e3..d96cc487d5 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb @@ -9,15 +9,16 @@ description = """OSU Micro-Benchmarks""" toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$MPICC"' -modextrapaths = {'PATH': ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']]} +benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': benchmark_dirs} sanity_check_paths = { 'files': [], - 'dirs': ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']], + 'dirs': benchmark_dirs, } moduleclass = 'perf' -- GitLab From 933b3512596586cc396eda8173c4dd00a48ec830 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 8 Jul 2015 09:44:29 +0300 Subject: [PATCH 877/992] Changes to config file and makefile patch --- easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb index e7342e0349..1318374418 100644 --- a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TGZ] skipsteps = ['configure'] -installopts = "INSTALL_DIR=%(installdir)s" +installopts = "DESTDIR=%(installdir)s" patches = [ 'BSMAP-2.74_makefile-modif.patch', diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch index 7992065109..daf84a74d5 100644 --- a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch @@ -1,5 +1,5 @@ Patch to point to the correct bin directory in the EASYBUILDINSTALLDIR and to -the correct location of the ZLIB libraries +to the correct location of the ZLIB libraries Thekla Loizou July 2015 --- bsmap-2.74/makefile.orig 2012-09-20 23:01:57.000000000 +0300 +++ bsmap-2.74/makefile 2014-12-16 09:24:16.033631393 +0200 @@ -7,7 +7,7 @@ Thekla Loizou July 2015 CC= g++ -BIN = $(DESTDIR)/usr/bin -+BIN=$(INSTALL_DIR)/bin ++BIN = $(DESTDIR)/bin FLAGS= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 #FLAGS= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -Wall -Wno-strict-aliasing -m64 -- GitLab From ecd27c7f809de416f719c86e86a9e13cfc4483e6 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 8 Jul 2015 11:09:47 +0200 Subject: [PATCH 878/992] Add minimal example easyconfig for SystemCompiler easyblock --- easybuild/easyconfigs/g/GCC/GCC-system.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-system.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb new file mode 100644 index 0000000000..c90402823f --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -0,0 +1,19 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: 3-clause BSD +## + +easyblock = 'SystemCompiler' + +name = "GCC" +version = "system" + +homepage = "" +description = "" # will be defined by the SystemCompiler easyblock when left empty or provide a custom description + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +moduleclass = 'compiler' -- GitLab From d2b7c9d32b3abff832ecd422f67352139ebec88a Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 8 Jul 2015 17:18:32 +0200 Subject: [PATCH 879/992] Provide homepage/description info in easyconfig file as requested --- easybuild/easyconfigs/g/GCC/GCC-system.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb index c90402823f..dcad754e21 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-system.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -11,8 +11,9 @@ easyblock = 'SystemCompiler' name = "GCC" version = "system" -homepage = "" -description = "" # will be defined by the SystemCompiler easyblock when left empty or provide a custom description +homepage = "http://gcc.gnu.org/" +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From 1620ca0634c3d85fb783b99d8272484e3f2ccb0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jul 2015 17:39:28 +0200 Subject: [PATCH 880/992] disable FTGL support, since it requires Mesa... --- .../easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb index f239ad58fc..e763143dc4 100644 --- a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb @@ -33,7 +33,7 @@ builddependencies = [('CMake', '3.2.3')] start_dir = 'eman2' separate_build_dir = True -configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s" +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s -DENABLE_FTGL=OFF" sanity_check_paths = { 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', -- GitLab From af12ebae5b8619a6346f2c199fd972028c97c99c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jul 2015 19:14:08 +0200 Subject: [PATCH 881/992] disable FTGL support in all EMAN2 easyconfigs, since it requires Mesa... --- .../easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb index b7a9c16a5a..82523c603b 100644 --- a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb @@ -33,7 +33,7 @@ builddependencies = [('CMake', '3.2.3')] start_dir = 'eman2' separate_build_dir = True -configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s" +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s -DENABLE_FTGL=OFF" sanity_check_paths = { 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', -- GitLab From 603e52db023817ae3dbc772d90f3a85677ff1009 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jul 2015 20:14:48 +0200 Subject: [PATCH 882/992] include comment w.r.t. 'system' version --- easybuild/easyconfigs/g/GCC/GCC-system.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb index dcad754e21..2d2a4ac6aa 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-system.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -8,10 +8,13 @@ easyblock = 'SystemCompiler' -name = "GCC" -version = "system" +name = 'GCC' +# using 'system' as a version instructs the SystemCompiler easyblock to derive the actual compiler version, +# and define $EBVERSION* accordingly (yet generate a module named GCC/system); +# if an actual version is specified here, it will be checked against the version of the system compiler that was found +version = 'system' -homepage = "http://gcc.gnu.org/" +homepage = 'http://gcc.gnu.org/" description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -- GitLab From 2a1ed4a93d9ba0752c396db910673fe1cc2d7198 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Jul 2015 21:37:24 +0200 Subject: [PATCH 883/992] fix typo --- easybuild/easyconfigs/g/GCC/GCC-system.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb index 2d2a4ac6aa..b24177d713 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-system.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -14,7 +14,7 @@ name = 'GCC' # if an actual version is specified here, it will be checked against the version of the system compiler that was found version = 'system' -homepage = 'http://gcc.gnu.org/" +homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -- GitLab From a9cf7a544cb111145bffc25c3da39623d6378fc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jul 2015 10:26:31 +0200 Subject: [PATCH 884/992] rename to R-bundle-pbd --- .../R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 5 ++--- .../pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 0 2 files changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/r/{R-bundle => R-bundle-pbd}/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb (93%) rename easybuild/easyconfigs/r/{R-bundle => R-bundle-pbd}/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch (100%) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb similarity index 93% rename from easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb rename to easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb index 05e79faaa5..347e7c8f1e 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb @@ -1,10 +1,9 @@ easyblock = 'Bundle' -name = 'R-bundle' +name = 'R-bundle-pbd' version = '20150605' -bundlename = 'pbd' rver = '3.1.3' -versionsuffix = '-R-%s-%s' % (rver, bundlename) +versionsuffix = '-R-%s-%s' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" diff --git a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch similarity index 100% rename from easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch rename to easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch -- GitLab From 9fd3633bc392130237f3b8c67fdc943c9d3e5ffc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jul 2015 11:25:21 +0200 Subject: [PATCH 885/992] fix typo --- .../r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb index 347e7c8f1e..002b4a69ed 100644 --- a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb @@ -3,7 +3,7 @@ easyblock = 'Bundle' name = 'R-bundle-pbd' version = '20150605' rver = '3.1.3' -versionsuffix = '-R-%s-%s' % rver +versionsuffix = '-R-%s' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" -- GitLab From a4ef0fa2041d1624f9c5932f87fdd443f73804a3 Mon Sep 17 00:00:00 2001 From: Niek de Klein Date: Fri, 10 Jul 2015 12:59:00 +0200 Subject: [PATCH 886/992] Delete zlib-1.2.7-goolf-1.7.20.eb --- .../z/zlib/zlib-1.2.7-goolf-1.7.20.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb deleted file mode 100644 index 3ae9b5cf4b..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolf-1.7.20.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.7' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, -not covered by any patents -- lossless data-compression library for use on virtually any -computer hardware and operating system.""" - -toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' -- GitLab From 8c2daaba9f64292d87f2addc7c30961628485101 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jul 2015 13:00:10 +0200 Subject: [PATCH 887/992] {system}[*/2015a] OpenSSL 1.0.1p --- .../o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 24 +++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb new file mode 100644 index 0000000000..ca15409515 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1p' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-%(version)s_fix-parallel.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb new file mode 100644 index 0000000000..8317b28f02 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1p' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-%(version)s_fix-parallel.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From 7108f2596f827aee80af6fbf9e140c9c44edb975 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jul 2015 13:02:48 +0200 Subject: [PATCH 888/992] fix patch specs in OpenSSL 1.0.1p easyconfigs --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 4 ++-- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb index ca15409515..7f6643b5da 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -13,8 +13,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] patches = [ - 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-%(version)s_fix-parallel.patch', + 'OpenSSL-1.0.1m_icc-fixes.patch', + 'OpenSSL-1.0.1m_fix-parallel.patch', ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb index 8317b28f02..99325fdaf7 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb @@ -13,8 +13,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] patches = [ - 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-%(version)s_fix-parallel.patch', + 'OpenSSL-1.0.1m_icc-fixes.patch', + 'OpenSSL-1.0.1m_fix-parallel.patch', ] dependencies = [('zlib', '1.2.8')] -- GitLab From bc738e41f70dc3c772033ac47fc9b9129b75d582 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Jul 2015 10:39:21 +0200 Subject: [PATCH 889/992] style fixes in CMake easyconfigs --- easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb | 8 +++++--- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 8 +++++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb index 5a9f80d2eb..e6f905f409 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -14,9 +14,11 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' -dependencies = [('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index 4a3f0c85e2..5e1447f0f0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -14,9 +14,11 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' -dependencies = [('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -- GitLab From 9135c9396f881a39102710e627dcedfb91e61bf0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Jul 2015 14:07:47 +0200 Subject: [PATCH 890/992] fix patches for OpenSSL 1.0.1p --- .../o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb | 5 +- .../o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch | 100 ++++++++++++++++++ 3 files changed, 102 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb index 7f6643b5da..6800732437 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -12,10 +12,7 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = [ - 'OpenSSL-1.0.1m_icc-fixes.patch', - 'OpenSSL-1.0.1m_fix-parallel.patch', -] +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb index 99325fdaf7..9e06d07cee 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb @@ -12,10 +12,7 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = [ - 'OpenSSL-1.0.1m_icc-fixes.patch', - 'OpenSSL-1.0.1m_fix-parallel.patch', -] +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch new file mode 100644 index 0000000000..4609252d6d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch @@ -0,0 +1,100 @@ +diff -ru openssl-1.0.1p.orig/Configure openssl-1.0.1p/Configure +--- openssl-1.0.1p.orig/Configure 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/Configure 2015-07-11 14:02:52.000000000 +0200 +@@ -351,7 +351,7 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-O3 -Wall::-D_REENTRANT::-ldl:BN_LLONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${armv4_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + #### IA-32 targets... +-"linux-ia32-icc", "icc:-DL_ENDIAN -O2 -no_cpprt::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia32-icc", "icc:-DL_ENDIAN -O2::-D_REENTRANT::-ldl -no_cpprt:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-elf", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -Wall::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-aout", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### +@@ -359,8 +359,9 @@ + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ia64-ecc","ecc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", ++"linux-x86_64-icc", "icc:-DL_ENDIAN -DTERMIO -O2::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux64-s390x", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1416,6 +1417,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1423,13 +1425,18 @@ + } + if ($iccver>=9) + { +- $cflags.=" -i-static"; +- $cflags=~s/\-no_cpprt/-no-cpprt/; ++ $lflags.=" -i-static"; ++ $lflags=~s/\-no_cpprt/-no-cpprt/; + } + if ($iccver>=10) + { +- $cflags=~s/\-i\-static/-static-intel/; ++ $lflags=~s/\-i\-static/-static-intel/; + } ++ if ($iccver>=11) ++ { ++ $cflags.=" -no-intel-extensions"; # disable Cilk ++ $lflags=~s/\-no\-cpprt/-no-cxxlib/; ++ } + } + + # Unlike other OSes (like Solaris, Linux, Tru64, IRIX) BSD run-time +diff -ru openssl-1.0.1p.orig/crypto/aes/aes_x86core.c openssl-1.0.1p/crypto/aes/aes_x86core.c +--- openssl-1.0.1p.orig/crypto/aes/aes_x86core.c 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/aes/aes_x86core.c 2015-07-11 14:02:52.000000000 +0200 +@@ -89,8 +89,10 @@ + #endif + + #undef ROTATE +-#if defined(_MSC_VER) || defined(__ICC) ++#if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++#elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1p.orig/crypto/des/des_locl.h openssl-1.0.1p/crypto/des/des_locl.h +--- openssl-1.0.1p.orig/crypto/des/des_locl.h 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/des/des_locl.h 2015-07-11 14:02:52.000000000 +0200 +@@ -162,8 +162,10 @@ + } \ + } + +-# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE(a,n) (_lrotr(a,n)) ++#elif defined(__ICC) ++#define ROTATE(a,n) (_rotr(a,n)) + # elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1p.orig/crypto/rc5/rc5_locl.h openssl-1.0.1p/crypto/rc5/rc5_locl.h +--- openssl-1.0.1p.orig/crypto/rc5/rc5_locl.h 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/rc5/rc5_locl.h 2015-07-11 14:02:52.000000000 +0200 +@@ -146,9 +146,12 @@ + *((c)++)=(unsigned char)(((l)>> 8L)&0xff), \ + *((c)++)=(unsigned char)(((l) )&0xff)) + +-#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE_l32(a,n) _lrotl(a,n) + # define ROTATE_r32(a,n) _lrotr(a,n) ++#elif defined(__ICC) ++#define ROTATE_l32(a,n) _rotl(a,n) ++#define ROTATE_r32(a,n) _rotr(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE_l32(a,n) ({ register unsigned int ret; \ -- GitLab From 3ead61ff878dde0a4fb678d7a2f9f78bbe92ea00 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Jul 2015 00:07:18 +0200 Subject: [PATCH 891/992] style fixes in eudev easyconfigs --- easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb | 4 ++-- easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb index 3efae98cdb..a1c5928f0b 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb @@ -20,10 +20,10 @@ builddependencies = [ ('gperf', '3.0.4'), ] -osdependencies = [('kernel-headers','linux-libc-dev')] +osdependencies = [('kernel-headers', 'linux-libc-dev')] configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' -preinstallopts = "make check && " +runtest = 'check' sanity_check_paths = { 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb index 9ada9135c9..5108981bdd 100644 --- a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb @@ -20,10 +20,10 @@ builddependencies = [ ('gperf', '3.0.4'), ] -osdependencies = [('kernel-headers','linux-libc-dev')] +osdependencies = [('kernel-headers', 'linux-libc-dev')] configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' -preinstallopts = "make check && " +runtest = 'check' sanity_check_paths = { 'files' : ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], -- GitLab From 7df1044fa78375edf24fcade7b335439bb3ace0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 12:16:45 +0200 Subject: [PATCH 892/992] rename BuildEnv-defaults to buildenv-default --- .../b/BuildEnv/BuildEnv-defaults-intel-2015a.eb | 13 ------------- .../b/buildenv/buildenv-default-intel-2015a.eb | 13 +++++++++++++ 2 files changed, 13 insertions(+), 13 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb diff --git a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb b/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb deleted file mode 100644 index 7e91b365f2..0000000000 --- a/easybuild/easyconfigs/b/BuildEnv/BuildEnv-defaults-intel-2015a.eb +++ /dev/null @@ -1,13 +0,0 @@ -easyblock = "BuildEnv" - -name = 'BuildEnv' -version = 'defaults' - -homepage = 'None' -description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you - can use to easily transition between toolchains when building your software. To query the variables being set please use: - module show """ - -toolchain = {'name': 'intel', 'version': '2015a'} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb new file mode 100644 index 0000000000..0321acfcc5 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +moduleclass = 'devel' -- GitLab From d23a37d802a66b777295ea800ab349c1077efaa7 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 13 Jul 2015 12:34:55 +0200 Subject: [PATCH 893/992] Reintroduce tabs into patch file. --- ..._ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 54 +++++++++---------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch index ae54615b78..34eaf4da13 100644 --- a/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch +++ b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch @@ -1,45 +1,45 @@ # Add support for intel mpi by removing references to BI_COMM_WORLD # BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. ---- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 -+++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 +--- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 ++++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 @@ -25,7 +25,9 @@ - BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; - BLACS_APTS.BI_MyContxts = BI_MyContxts; - BLACS_APTS.BI_SysContxts = BI_SysContxts; + BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; + BLACS_APTS.BI_MyContxts = BI_MyContxts; + BLACS_APTS.BI_SysContxts = BI_SysContxts; +#ifndef __INTEL_COMPILER - BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; + BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; +#endif - BLACS_APTS.BI_Stats = BI_Stats; + BLACS_APTS.BI_Stats = BI_Stats; - #if (BLACS_APTS_DEBUG & 1) == 1 + #if (BLACS_APTS_DEBUG & 1) == 1 @@ -44,7 +46,9 @@ - BI_AuxBuff.nAops, BI_AuxBuff.N); - REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, - &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + BI_AuxBuff.nAops, BI_AuxBuff.N); + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); +#ifndef __INTEL_COMPILER - REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, +#endif - BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); - REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, - BI_Stats); + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); @@ -89,7 +93,9 @@ - BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; - BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; + BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; + BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; +#ifndef __INTEL_COMPILER - BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; + BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; +#endif - BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; + BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; - #if (BLACS_APTS_DEBUG & 1) == 1 + #if (BLACS_APTS_DEBUG & 1) == 1 @@ -109,7 +115,9 @@ - REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, - &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); - REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, +#ifndef __INTEL_COMPILER - BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); +#endif - REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, - BI_Stats); - } + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); + } -- GitLab From b6efe47eda0ac187c3b843fb2d47080ec4eb67dd Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 13 Jul 2015 12:45:40 +0200 Subject: [PATCH 894/992] Remove old file path. --- ...bundle-20150605-intel-2015a-R-3.1.3-pbd.eb | 45 ------------------- ..._ignore-BI_COMM_GLOBAL-for-intel-mpi.patch | 45 ------------------- 2 files changed, 90 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb delete mode 100644 easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb deleted file mode 100644 index 05e79faaa5..0000000000 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'Bundle' - -name = 'R-bundle' -version = '20150605' -bundlename = 'pbd' -rver = '3.1.3' -versionsuffix = '-R-%s-%s' % (rver, bundlename) - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -# these are extensions for R -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -dependencies = [ - ('R', rver), -] - -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': name_tmpl, -} - -# !! order of packages is important !! -exts_list = [ - ('pbdMPI', '0.2-5', ext_options), - ('pbdSLAP', '0.2-0', ext_options), - ('pbdBASE', '0.2-3', dict(ext_options.items() + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), - ('pbdDMAT', '0.2-3', ext_options), - ('pbdDEMO', '0.2-0', ext_options), - ('pmclust', '0.1-6', ext_options), - ('EMCluster', '0.2-4', ext_options), -] - -modextrapaths = {'R_LIBS': ''} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch deleted file mode 100644 index ae54615b78..0000000000 --- a/easybuild/easyconfigs/r/R-bundle/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch +++ /dev/null @@ -1,45 +0,0 @@ -# Add support for intel mpi by removing references to BI_COMM_WORLD -# BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. ---- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 -+++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 -@@ -25,7 +25,9 @@ - BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; - BLACS_APTS.BI_MyContxts = BI_MyContxts; - BLACS_APTS.BI_SysContxts = BI_SysContxts; -+#ifndef __INTEL_COMPILER - BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; -+#endif - BLACS_APTS.BI_Stats = BI_Stats; - - #if (BLACS_APTS_DEBUG & 1) == 1 -@@ -44,7 +46,9 @@ - BI_AuxBuff.nAops, BI_AuxBuff.N); - REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, - &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); -+#ifndef __INTEL_COMPILER - REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, -+#endif - BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); - REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, - BI_Stats); -@@ -89,7 +93,9 @@ - - BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; - BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; -+#ifndef __INTEL_COMPILER - BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; -+#endif - BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; - - #if (BLACS_APTS_DEBUG & 1) == 1 -@@ -109,7 +115,9 @@ - REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, - &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); - REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, -+#ifndef __INTEL_COMPILER - BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); -+#endif - REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, - BI_Stats); - } - -- GitLab From 642bfe59dfeade76094a635195dbf906d704d6e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 12:51:14 +0200 Subject: [PATCH 895/992] include Tcl/Tk dependencies in R 3.2.0 easyconfig --- easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb index cf66631597..fb02153585 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] exts_list = [] -- GitLab From 030501ad94e6cb0e4ba7f90aae463c4e8852cb1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 12:59:53 +0200 Subject: [PATCH 896/992] add Tcl/Tk as dependencies in R 3.2.0 easyconfig --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 ++ .../t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb | 24 ++++++++++++++++++ 3 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 93ecdc515d..69f979e2b7 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] name_tmpl = '%(name)s_%(version)s.tar.gz' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..e2124cc24d --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb new file mode 100644 index 0000000000..5d72cc8d79 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From e220e175644efd2cb8194a7498a195808f11e7fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 13:15:55 +0200 Subject: [PATCH 897/992] bump versions of Bioconductor pkgs --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 53 +++++++++---------- 1 file changed, 25 insertions(+), 28 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 69f979e2b7..7c7cafbc81 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -219,16 +219,16 @@ exts_list = [ ('R.matlab', '3.2.0', ext_options), ('BiocGenerics', '0.14.0', bioconductor_options), ('Biobase', '2.28.0', bioconductor_options), - ('S4Vectors', '0.6.0', bioconductor_options), - ('IRanges', '2.2.1', bioconductor_options), - ('GenomeInfoDb', '1.4.0', bioconductor_options), - ('AnnotationDbi', '1.30.0', bioconductor_options), + ('S4Vectors', '0.6.1', bioconductor_options), + ('IRanges', '2.2.5', bioconductor_options), + ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.0', bioconductor_options), - ('GenomicRanges', '1.20.3', bioconductor_options), - ('Rsamtools', '1.20.1', bioconductor_options), - ('BiocParallel', '1.2.0', bioconductor_options), + ('Biostrings', '2.36.1', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('BiocParallel', '1.2.9', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), ('ShortRead', '1.26.0', bioconductor_options), ('graph', '1.46.0', bioconductor_options), @@ -310,19 +310,19 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.36.0', bioconductor_options), - ('BiocInstaller', '1.18.1', bioconductor_options), + ('BiocInstaller', '1.18.3', bioconductor_options), ('preprocessCore', '1.30.0', bioconductor_options), - ('affy', '1.46.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.1', bioconductor_options), + ('limma', '3.24.13', bioconductor_options), ('RBGL', '1.44.0', bioconductor_options), ('org.Hs.eg.db', '3.1.2', bioconductor_options), - ('AnnotationForge', '1.10.0', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), ('KEGG.db', '3.1.2', bioconductor_options), ('annaffy', '1.40.0', bioconductor_options), ('gcrma', '2.40.0', bioconductor_options), ('oligoClasses', '1.30.0', bioconductor_options), - ('edgeR', '3.10.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), ('PFAM.db', '3.1.2', bioconductor_options), ('locfit', '1.5-9.1', ext_options), ('gridExtra', '0.9.1', ext_options), @@ -365,7 +365,7 @@ exts_list = [ ('genoset', '1.22.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '1.0.2', ext_options), - ('NOISeq', '2.10.0', bioconductor_options), + ('NOISeq', '2.12.0', bioconductor_options), ('openxlsx', '2.4.0', ext_options), ('Rgraphviz', '2.12.0', bioconductor_options), ('pvclust', '1.3-2', ext_options), @@ -376,25 +376,22 @@ exts_list = [ ('xlsx', '0.5.7', ext_options), ('XML', '3.98-1.1', ext_options), ('biomaRt', '2.24.0', bioconductor_options), - ('annotate', '1.46.0', bioconductor_options), - ('GSEABase', '1.30.1', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), ('genefilter', '1.50.0', bioconductor_options), - ('Category', '2.34.0', bioconductor_options), - ('org.Hs.eg.db', '3.1.2', bioconductor_options), - ('AnnotationForge', '1.10.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('rtracklayer', '1.28.2', bioconductor_options), - ('GenomicFeatures', '1.20.0', bioconductor_options), - ('BSgenome', '1.36.0', bioconductor_options), - ('VariantAnnotation', '1.14.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), + ('BSgenome', '1.36.2', bioconductor_options), + ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), ('ggbio', '1.16.0', bioconductor_options), ('geneplotter', '1.46.0', bioconductor_options), - ('DESeq2', '1.8.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), ('ReportingTools', '2.8.0', bioconductor_options), - ('genefilter', '1.50.0', bioconductor_options), - ('affycoretools', '1.40.1', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), ('Homo.sapiens', '1.1.2', bioconductor_options), ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), @@ -408,13 +405,13 @@ exts_list = [ ('KEGGprofile', '1.10.0', bioconductor_options), ('minfi', '1.14.0', bioconductor_options), ('methylumi', '2.14.0', bioconductor_options), - ('lumi', '2.20.1', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), ('widgetTools', '1.46.0', bioconductor_options), ('tkWidgets', '1.46.0', bioconductor_options), ('Mfuzz', '2.28.0', bioconductor_options), ('maSigPro', '1.40.0', bioconductor_options), ('SPIA', '2.20.0', bioconductor_options), - ('Gviz', '1.12.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), -- GitLab From d7e28ea23262a7532e44dde55a0035e59890567a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 14:27:22 +0200 Subject: [PATCH 898/992] bump version of hgu133plus2.db --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 7c7cafbc81..28b28e0dba 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -347,7 +347,7 @@ exts_list = [ ('trimcluster', '0.1-2', ext_options), ('fpc', '2.1-9', ext_options), ('BiasedUrn', '1.06.1', ext_options), - ('hgu133plus2.db', '3.1.2', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), ('TeachingDemos', '2.9', ext_options), ('jsonlite', '0.9.16', ext_options), ('kohonen', '2.0.18', ext_options), -- GitLab From 38d5bbb0bef54572add45272316cf5dc36fdf076 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 14:48:17 +0200 Subject: [PATCH 899/992] split off Bioconductor packages into a separate easyconfig --- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 93 ------------------- 1 file changed, 93 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 28b28e0dba..4395bd8986 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -33,18 +33,6 @@ ext_options = { ], 'source_tmpl': name_tmpl, } -# Bioconductor packages have a different download url -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} # !! order of packages is important !! @@ -217,21 +205,6 @@ exts_list = [ ('cgdsr', '1.1.33', ext_options), ('R.utils', '2.0.1', ext_options), ('R.matlab', '3.2.0', ext_options), - ('BiocGenerics', '0.14.0', bioconductor_options), - ('Biobase', '2.28.0', bioconductor_options), - ('S4Vectors', '0.6.1', bioconductor_options), - ('IRanges', '2.2.5', bioconductor_options), - ('GenomeInfoDb', '1.4.1', bioconductor_options), - ('AnnotationDbi', '1.30.1', bioconductor_options), - ('XVector', '0.8.0', bioconductor_options), - ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.1', bioconductor_options), - ('GenomicRanges', '1.20.5', bioconductor_options), - ('Rsamtools', '1.20.4', bioconductor_options), - ('BiocParallel', '1.2.9', bioconductor_options), - ('GenomicAlignments', '1.4.1', bioconductor_options), - ('ShortRead', '1.26.0', bioconductor_options), - ('graph', '1.46.0', bioconductor_options), ('gbm', '2.1.1', ext_options), ('dichromat', '2.0-0', ext_options), ('Formula', '1.2-1', ext_options), @@ -309,32 +282,13 @@ exts_list = [ ('optparse', '1.3.0', ext_options), ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), - ('affyio', '1.36.0', bioconductor_options), - ('BiocInstaller', '1.18.3', bioconductor_options), - ('preprocessCore', '1.30.0', bioconductor_options), - ('affy', '1.46.1', bioconductor_options), - ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.13', bioconductor_options), - ('RBGL', '1.44.0', bioconductor_options), - ('org.Hs.eg.db', '3.1.2', bioconductor_options), - ('AnnotationForge', '1.10.1', bioconductor_options), - ('KEGG.db', '3.1.2', bioconductor_options), - ('annaffy', '1.40.0', bioconductor_options), - ('gcrma', '2.40.0', bioconductor_options), - ('oligoClasses', '1.30.0', bioconductor_options), - ('edgeR', '3.10.2', bioconductor_options), - ('PFAM.db', '3.1.2', bioconductor_options), ('locfit', '1.5-9.1', ext_options), ('gridExtra', '0.9.1', ext_options), ('GGally', '0.5.0', ext_options), - ('baySeq', '2.2.0', bioconductor_options), ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), - ('qvalue', '2.0.0', bioconductor_options), - ('impute', '1.42.0', bioconductor_options), ('matrixStats', '0.14.0', ext_options), ('samr', '2.0', ext_options), - ('DEGseq', '1.22.0', bioconductor_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), @@ -347,72 +301,25 @@ exts_list = [ ('trimcluster', '0.1-2', ext_options), ('fpc', '2.1-9', ext_options), ('BiasedUrn', '1.06.1', ext_options), - ('hgu133plus2.db', '3.1.3', bioconductor_options), ('TeachingDemos', '2.9', ext_options), ('jsonlite', '0.9.16', ext_options), ('kohonen', '2.0.18', ext_options), ('base64', '1.1', ext_options), - ('illuminaio', '0.10.0', bioconductor_options), ('registry', '0.2', ext_options), ('pkgmaker', '0.22', ext_options), ('rngtools', '1.2.4', ext_options), ('doRNG', '1.6', ext_options), - ('bumphunter', '1.8.0', bioconductor_options), - ('multtest', '2.24.0', bioconductor_options), - ('siggenes', '1.42.0', bioconductor_options), ('nleqslv', '2.7', ext_options), - ('DynDoc', '1.46.0', bioconductor_options), - ('genoset', '1.22.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '1.0.2', ext_options), - ('NOISeq', '2.12.0', bioconductor_options), ('openxlsx', '2.4.0', ext_options), - ('Rgraphviz', '2.12.0', bioconductor_options), ('pvclust', '1.3-2', ext_options), ('RCircos', '1.1.2', ext_options), - ('RNASeqPower', '1.8.0', bioconductor_options), ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('XML', '3.98-1.1', ext_options), - ('biomaRt', '2.24.0', bioconductor_options), - ('annotate', '1.46.1', bioconductor_options), - ('GSEABase', '1.30.2', bioconductor_options), - ('genefilter', '1.50.0', bioconductor_options), - ('Category', '2.34.2', bioconductor_options), - ('GOstats', '2.34.0', bioconductor_options), - ('rtracklayer', '1.28.6', bioconductor_options), - ('GenomicFeatures', '1.20.1', bioconductor_options), - ('BSgenome', '1.36.2', bioconductor_options), - ('VariantAnnotation', '1.14.6', bioconductor_options), - ('biovizBase', '1.16.0', bioconductor_options), - ('OrganismDbi', '1.10.0', bioconductor_options), - ('ggbio', '1.16.0', bioconductor_options), - ('geneplotter', '1.46.0', bioconductor_options), - ('DESeq2', '1.8.1', bioconductor_options), - ('ReportingTools', '2.8.0', bioconductor_options), - ('affycoretools', '1.40.5', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), - ('Homo.sapiens', '1.1.2', bioconductor_options), - ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), - ('AgiMicroRna', '2.18.0', bioconductor_options), - ('GenomeGraphs', '1.28.0', bioconductor_options), - ('geneLenDataBase', '1.4.0', bioconductor_options), - ('goseq', '1.20.0', bioconductor_options), ('httr', '0.6.1', ext_options), - ('KEGGREST', '1.8.0', bioconductor_options), - ('KEGGgraph', '1.26.0', bioconductor_options), - ('KEGGprofile', '1.10.0', bioconductor_options), - ('minfi', '1.14.0', bioconductor_options), - ('methylumi', '2.14.0', bioconductor_options), - ('lumi', '2.20.2', bioconductor_options), - ('widgetTools', '1.46.0', bioconductor_options), - ('tkWidgets', '1.46.0', bioconductor_options), - ('Mfuzz', '2.28.0', bioconductor_options), - ('maSigPro', '1.40.0', bioconductor_options), - ('SPIA', '2.20.0', bioconductor_options), - ('Gviz', '1.12.1', bioconductor_options), - ('cummeRbund', '2.10.0', bioconductor_options), ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), ('tensor', '1.5', ext_options), -- GitLab From acdd5f8ffc2be122a82d57e81f307d25da1ef9cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 14:49:51 +0200 Subject: [PATCH 900/992] actually add R-bundle-Bioconductor easyconfig --- ...e-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 124 ++++++++++++++++++ 1 file changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb new file mode 100644 index 0000000000..88053df714 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -0,0 +1,124 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +rver = '3.2.0' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', rver)] + +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.1', bioconductor_options), + ('IRanges', '2.2.5', bioconductor_options), + ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.1', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('BiocParallel', '1.2.9', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.3', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.13', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), + ('baySeq', '2.2.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), + ('DEGseq', '1.22.0', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), + ('NOISeq', '2.12.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), + ('BSgenome', '1.36.2', bioconductor_options), + ('VariantAnnotation', '1.14.6', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.0', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['RCurl', 'XML', 'spliceR'], +} + +moduleclass = 'lang' -- GitLab From 374ade892abc2308b2275c28f24f31e06e406ce8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 14:58:14 +0200 Subject: [PATCH 901/992] fix sanity check --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 88053df714..2e05c29673 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -118,7 +118,7 @@ modextrapaths = {'R_LIBS': ''} sanity_check_paths = { 'files': [], - 'dirs': ['RCurl', 'XML', 'spliceR'], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], } moduleclass = 'lang' -- GitLab From 7d4512368e615e99bd4e4205a62a576ed8628421 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 15:02:31 +0200 Subject: [PATCH 902/992] downgrade Java to 1.7.0_80 --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 4395bd8986..0b3a34bd3f 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ] -- GitLab From e8a33bbd0b50c0b42eec0ed235c4135cf7126001 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 15:08:36 +0200 Subject: [PATCH 903/992] {lang}[dummy] Java 1.8.0_45 --- easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb new file mode 100644 index 0000000000..50a687a050 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_45' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 726b83763fcf15e22faa18698cf3847ce89dbc3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 15:10:28 +0200 Subject: [PATCH 904/992] {lib}[intel/2015a] libjpeg-turbo 1.4.1 --- .../libjpeg-turbo-1.4.1-intel-2015a.eb | 24 ++++++++++++++ .../n/NASM/NASM-2.11.08-intel-2015a.eb | 31 +++++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb new file mode 100644 index 0000000000..3f922516d9 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.1' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb new file mode 100644 index 0000000000..77ceaa2d9a --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 6d9d4dc75af37146c1c9658db60af889c5b7270b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:36:56 +0200 Subject: [PATCH 905/992] add cURL/libxml2 deps + RCurl lib --- .../c/cURL/cURL-7.43.0-goolf-1.7.20.eb | 29 +++++++++++++++++++ .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 4 ++- 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..8a52b67eb0 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 0b3a34bd3f..c303899088 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -22,6 +22,8 @@ dependencies = [ ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -329,8 +331,8 @@ exts_list = [ ('rgeos', '0.3-8', ext_options), ('gdalUtils', '0.3.1', ext_options), ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), ('bio3d', '2.2-2', ext_options), - ] moduleclass = 'lang' -- GitLab From 40fbd81ee8900e43f38100d1b7723ee78655e065 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:41:30 +0200 Subject: [PATCH 906/992] add missing deps --- .../c/cURL/cURL-7.43.0-intel-2015a.eb | 29 +++++++++++++++++++ .../l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb | 28 ++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb new file mode 100644 index 0000000000..e4763fc7a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..906e3a297c --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' -- GitLab From 722898b7de41ab85e827519c6713a8403a439e9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:44:50 +0200 Subject: [PATCH 907/992] kick out cURL intel/2015a easyconfig --- .../c/cURL/cURL-7.43.0-intel-2015a.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb deleted file mode 100644 index e4763fc7a1..0000000000 --- a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'cURL' -version = '7.43.0' - -homepage = 'http://curl.haxx.se' -description = """libcurl is a free and easy-to-use client-side URL transfer library, - supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, - POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports - SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, - proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, - Kerberos), file transfer resume, http proxy tunneling and more.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://curl.haxx.se/download/'] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# dependencies = [('OpenSSL', '1.0.1p')] -# configopts = "--with-ssl=$EBROOTOPENSSL" - -sanity_check_paths = { - 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'tools' -- GitLab From 02b044da3f765afa44b268f0cbcea3afd05c0182 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:45:57 +0200 Subject: [PATCH 908/992] add OpenSSL easyconfig --- .../o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb new file mode 100644 index 0000000000..2e714a6aff --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From 0cc773f51fc1999c9e19b57e8fb3a42bb94adbba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 16:46:49 +0200 Subject: [PATCH 909/992] {lang}[intel/2015a] R v3.2.1 --- .../c/cURL/cURL-7.43.0-intel-2015a.eb | 29 ++ .../easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 340 ++++++++++++++++++ 2 files changed, 369 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb new file mode 100644 index 0000000000..e4763fc7a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb new file mode 100644 index 0000000000..cd0b403c28 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -0,0 +1,340 @@ +name = 'R' +version = '3.2.1' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.8.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.0.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.58.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.0', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-10', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.5-12', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-31', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-2', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.6', ext_options), + ('RcppArmadillo', '0.5.200.1.0', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-42', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-13', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-10', ext_options), + ('nlme', '3.1-121', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('quantreg', '5.11', ext_options), + ('mgcv', '1.8-6', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-4', ext_options), + ('sp', '1.1-1', ext_options), + ('vcd', '1.4-1', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-10', ext_options), + ('mice', '2.22', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.2', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-65', ext_options), + ('survival', '2.38-3', ext_options), + ('gam', '1.12', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('zoo', '1.7-12', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('lmtest', '0.9-34', ext_options), + ('mnormt', '1.5-3', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-3', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-10', ext_options), + ('VGAM', '0.9-8', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.12', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.1.33', ext_options), + ('R.utils', '2.1.0', ext_options), + ('R.matlab', '3.2.0', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('reshape2', '1.4.1', ext_options), + ('gtable', '0.1.2', ext_options), + ('scales', '0.2.5', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '1.0.1', ext_options), + ('Hmisc', '3.16-0', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-47', ext_options), + ('data.table', '1.9.4', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.3', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.1.0', ext_options), + ('shiny', '0.12.1', ext_options), + ('adegenet', '2.0.0', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.4-15', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '2.0-2', ext_options), + ('labdsv', '1.7-0', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.11', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('rms', '4.3-1', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('knitr', '1.10.5', ext_options), + ('statmod', '1.4.21', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.14.2', ext_options), + ('samr', '2.0', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('FactoMineR', '1.31.3', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', 'Finite', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.8', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.7', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('XML', '3.98-1.3', ext_options), + ('httr', '1.0.0', ext_options), + ('maptools', '0.8-36', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.42-2', ext_options), + ('rgeos', '0.3-11', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-2', ext_options), + ('doParallel', '1.0.8', ext_options), + ('interpretR', '0.2.3', ext_options), +] + +moduleclass = 'lang' -- GitLab From 4ff33aeeb65ac1304c47a5205defa099ec495690 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 21:45:27 +0200 Subject: [PATCH 910/992] fix flexmix version in R 3.2.1 easyconfig --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index cd0b403c28..4600a51eeb 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -297,7 +297,7 @@ exts_list = [ ('FactoMineR', '1.31.3', ext_options), ('modeltools', '0.2-21', ext_options), ('flexclust', '1.3-4', ext_options), - ('flexmix', 'Finite', ext_options), + ('flexmix', '2.3-13', ext_options), ('prabclus', '2.2-6', ext_options), ('diptest', '0.75-7', ext_options), ('trimcluster', '0.1-2', ext_options), -- GitLab From ad0f2adaaf4baab4a102e1060f25e5fedce7d11a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:21:37 +0200 Subject: [PATCH 911/992] add patch for geometry R extension + add missing extensions (fpp & co) --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 4600a51eeb..33b6f91f96 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -56,7 +56,7 @@ exts_list = [ ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), - ('geometry', '0.3-5', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), ('bit', '1.1-12', ext_options), ('filehash', '2.2-2', ext_options), ('ff', '2.2-13', ext_options), @@ -335,6 +335,10 @@ exts_list = [ ('bio3d', '2.2-2', ext_options), ('doParallel', '1.0.8', ext_options), ('interpretR', '0.2.3', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' -- GitLab From 5233500a63dc309fd18132cfa53ad185b69b67e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:34:30 +0200 Subject: [PATCH 912/992] fix templating issues --- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb | 2 +- easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb | 2 +- easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb | 2 +- easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb index 5cdf92f035..fa154ada7f 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb index 49d7098c87..558ae70b7f 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb index 6de0d3d8d3..0464a3968b 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb index 46c998562c..c9298da39e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb index b955c4abf7..8d4de54b7a 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index c9f730872f..fa2a08d015 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index 6866cddf63..fa449b6641 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb index 1ed83c4526..7dc3787320 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb @@ -32,7 +32,7 @@ with_configure = True graphlib_version = '0.3' preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version # build isoinfer, make sure we can link to libgraph.a -preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += "cd ../%(namelower)s-%(version)s && " preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version files_to_copy = [ diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb index 3f65089c09..436dd9a680 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb @@ -32,7 +32,7 @@ with_configure = True graphlib_version = '0.3' preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version # build isoinfer, make sure we can link to libgraph.a -preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += "cd ../%(namelower)s-%(version)s && " preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version files_to_copy = [ diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb index d22d8136b3..9346ee7b4c 100644 --- a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['SOURCEFORGE_SOURCE'] +source_urls = [SOURCEFORGE_SOURCE] builddependencies = [ ('Bison', '3.0.2'), diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb index 5101540bd3..0ad7f07069 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb @@ -32,7 +32,7 @@ dependencies = [ # RELION expects FLTK to be in external/fltk-1.3.0 configopts = ['--enable-mpi --enable-openmp && ln -s $EBROOTFLTK/include external/fltk-1.3.0'] buildopts = 'LIBS="-lfftw3_threads -lfftw3 -lm -lpthread -lfltk -lX11 -lXft -lfontconfig -lXext -lXinerama" ' -installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/relion " +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " sanity_check_paths = { 'files': ['bin/relion'], diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb index 7b003f1cbf..25abcbdcb9 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb @@ -34,7 +34,7 @@ dependencies = [ configopts = ['--enable-mpi --enable-openmp && ln -s $EBROOTFLTK/include external/fltk-1.3.0'] buildopts = 'LIBS="-lfftw3_threads -lfftw3 -lm -lpthread -lfltk -lX11 -lXft -lfontconfig -lXext -lXinerama" ' # users expect the maingui binary to be called relion -installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/relion " +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " moduleclass = 'bio' -- GitLab From bd8efd374826612f5e577a4e176d82c182f67fa0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:43:56 +0200 Subject: [PATCH 913/992] add extensions that dropped out --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index c303899088..0b8d49ad4e 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -320,6 +320,11 @@ exts_list = [ ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ('XML', '3.98-1.1', ext_options), ('httr', '0.6.1', ext_options), ('maptools', '0.8-36', ext_options), -- GitLab From e9890996ac06f8717cfb8d767c3fc63dc126c34f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:44:56 +0200 Subject: [PATCH 914/992] add missing vegan extension --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 33b6f91f96..602865ae41 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -320,6 +320,11 @@ exts_list = [ ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ('XML', '3.98-1.3', ext_options), ('httr', '1.0.0', ext_options), ('maptools', '0.8-36', ext_options), @@ -335,10 +340,6 @@ exts_list = [ ('bio3d', '2.2-2', ext_options), ('doParallel', '1.0.8', ext_options), ('interpretR', '0.2.3', ext_options), - ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), - ('fma', '2.01', ext_options), - ('expsmooth', '2.3', ext_options), - ('fpp', '0.5', ext_options), ] moduleclass = 'lang' -- GitLab From d10f4cf170b7f8b6af9350c8c1ca42f373863ed1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jul 2015 22:50:45 +0200 Subject: [PATCH 915/992] drop patch in OpenSSL, not need when icc is not used in toolchain --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb index 2e714a6aff..733ddd9ac4 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb @@ -12,8 +12,6 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.openssl.org/source/'] -patches = ['OpenSSL-%(version)s_icc-fixes.patch'] - dependencies = [('zlib', '1.2.8')] runtest = 'test' -- GitLab From f16a42c06203e45ec1326184dd2a73a0f4252221 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:29:13 +0200 Subject: [PATCH 916/992] bump version to 2.2.0 and update release notes --- RELEASE_NOTES | 52 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 52 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b593156524..da12db80a1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -4,7 +4,57 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. The latest version of easybuild-easyconfig provides 3,689 easyconfig files, for 611 different software packages, -33 different (compiler) toolchains and 8 software bundles. +33 different (compiler) toolchains and 12 software bundles. + +v2.2.0 (July 14th 2015) +----------------------- + +feature + bugfix release +- added example easyconfig files for XXX new software packages: + ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171), Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995), EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), frealign (#1619), FPM (#1440), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760), libXScrnSaver (#1653), MATIO (#1004), MuTect *#1483), ncdf (#617), NEMO (#1640), ngspice (#1116), ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412), Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776), rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658), SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot (#1100), Vampir (#512), VampirServer (#512), verifyBamID (#1675) +- added easyconfigs for 4 new software bundles: + R-bundle-Bioconductor (#1573), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), R-bundle-pbd (#1659) +- added easyconfigs for new GNU toolchain (#1346, #1669) +- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1, + Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1 +- various other enhancements, including: + - update all ncurses easyconfigs to enable ncursesw and use ConfigureMake easyblock (#1337) + - update PDT easyconfigs to use PDT easyblock (#1687) + - add custom sanity_check_paths in libxml2 easyconfigs (#1690) + - enhance unit tests to also cover EasyConfig.dump() method on all easyconfigs (#1761) + - include snappy as dependency in Hadoop easyconfigs (#1758, #1773) + - enable SSL support in CMake v3.2.3 easyconfigs (#1784) + - add additional extensions in R easyconfigs (#1637) +- various bug fixes, including: + - add patch file required for correct CUDA-aware OpenMPI v1.7.3 build (#631) + - fix issue with OpenMPI dependency in ECore easyconfigs (#777) + - don't run the Bloom tests for Jellyfish, they can randomly fail (#1016) + - fix source URLs in BioPerl easyconfigs (#1075) + - patch out svnversion command in Python 2.5.6 to fix build on recent systems (#1576) + - consistently use https for PyPI URLs in homepage/source_urls (#1616, #1722) + - include Tcl and Tk as dependencies in R easyconfig (#1623) + - add patch for installing paycheck as Py3 extension (#1629) + - add Perl dependency in git 2.x easyconfigs (#1631) + - fix easycofnig for GMP 6.0.0, don't use 6.0.0a sources (#1635) + - fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (#1652) + - include Tk as dependency in Python 2.7.9 easyconfigs (#1654) + - include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works (#1655) + - drop gpfs versionsuffix and stop using no longer existing --enable-gpfs configopt for recent HDF5 versions (#1657) + - include missing libxml2 dep in GLib easyconfigs (#1666) + - fix source URLs in Qt easyconfigs (#1673) + - fix source URLs for argparse Python extension (#1697) + - fix source URLs for deap Python extension (#1699) + - fix easyconfigs unit tests after making ModulesTool a non-singleton class (#1708) + - fix names for Xmipp easyconfigs and patches (#1719) + - add patch for Qt 4.8.6 to fix build issue on RHEL6 with intel/2015a (#1734) + - add M4 as build dep for GCC 5.1.0 (#1735) + - fix Bioconductor extension versions in R 3.1.3 easyconfigs (#1748) + - remove custom exts_filter definition from Python 3.4.3 easyconfig (#1765) + - fix source_urls in netCDF easyconfigs (#1766) + - fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (#1767) + - add Infiniband-related patch for OpenMPI versions < 1.8.6 (#1785) v2.1.1 (May 18th 2015) ---------------------- diff --git a/setup.py b/setup.py index 9e5dd5137c..d9262a0b8c 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.2.0dev' +VERSION = '2.2.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 8a6e8a5b0788bd4f277d2ab72540ce96bb161362 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:30:39 +0200 Subject: [PATCH 917/992] move up lmtest, as dep for vcd --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 602865ae41..89ab03d55c 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -151,6 +151,7 @@ exts_list = [ ('colorspace', '1.2-6', ext_options), ('robustbase', '0.92-4', ext_options), ('sp', '1.1-1', ext_options), + ('lmtest', '0.9-34', ext_options), ('vcd', '1.4-1', ext_options), ('snowfall', '1.84-6', ext_options), ('rpart', '4.1-10', ext_options), @@ -180,7 +181,6 @@ exts_list = [ ('xts', '0.9-7', ext_options), ('TTR', '0.23-0', ext_options), ('quantmod', '0.4-4', ext_options), - ('lmtest', '0.9-34', ext_options), ('mnormt', '1.5-3', ext_options), ('mvtnorm', '1.0-2', ext_options), ('pcaPP', '1.9-60', ext_options), -- GitLab From 9b2749fd7256544007f553f30660f52be6785250 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:33:05 +0200 Subject: [PATCH 918/992] move up zoo, as dep for lmtest --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 89ab03d55c..f64a491a30 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -151,6 +151,7 @@ exts_list = [ ('colorspace', '1.2-6', ext_options), ('robustbase', '0.92-4', ext_options), ('sp', '1.1-1', ext_options), + ('zoo', '1.7-12', ext_options), ('lmtest', '0.9-34', ext_options), ('vcd', '1.4-1', ext_options), ('snowfall', '1.84-6', ext_options), @@ -177,7 +178,6 @@ exts_list = [ ('gamlss.dist', '4.3-4', ext_options), ('hwriter', '1.3.2', ext_options), ('KernSmooth', '2.23-15', ext_options), - ('zoo', '1.7-12', ext_options), ('xts', '0.9-7', ext_options), ('TTR', '0.23-0', ext_options), ('quantmod', '0.4-4', ext_options), -- GitLab From 4e23b214781e1f190c912e01f53c004ac0f42784 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:52:20 +0200 Subject: [PATCH 919/992] move up munsell/labeling --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index f64a491a30..a5380b8605 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -213,12 +213,12 @@ exts_list = [ ('acepack', '1.3-3.3', ext_options), ('reshape2', '1.4.1', ext_options), ('gtable', '0.1.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), ('scales', '0.2.5', ext_options), ('proto', '0.3-10', ext_options), ('ggplot2', '1.0.1', ext_options), ('Hmisc', '3.16-0', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), ('fastcluster', '1.1.16', ext_options), ('chron', '2.3-47', ext_options), ('data.table', '1.9.4', ext_options), -- GitLab From 0dd9bb204b19b0fc0a267d9e8dc7253a05c0f296 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 00:57:06 +0200 Subject: [PATCH 920/992] move up gridExtra --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index a5380b8605..0c80677c6d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -218,6 +218,7 @@ exts_list = [ ('scales', '0.2.5', ext_options), ('proto', '0.3-10', ext_options), ('ggplot2', '1.0.1', ext_options), + ('gridExtra', '0.9.1', ext_options), ('Hmisc', '3.16-0', ext_options), ('fastcluster', '1.1.16', ext_options), ('chron', '2.3-47', ext_options), @@ -285,7 +286,6 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('locfit', '1.5-9.1', ext_options), - ('gridExtra', '0.9.1', ext_options), ('GGally', '0.5.0', ext_options), ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), -- GitLab From f46c1223efc8c5df3417884adb358a505ecbcfdd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:13:17 +0200 Subject: [PATCH 921/992] add missing NMF/irlba deps, move their deps up --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 0c80677c6d..646fb4f5a1 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -223,6 +223,11 @@ exts_list = [ ('fastcluster', '1.1.16', ext_options), ('chron', '2.3-47', ext_options), ('data.table', '1.9.4', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '1.0.3', ext_options), ('igraph', '1.0.1', ext_options), ('GeneNet', '1.2.12', ext_options), ('ape', '3.3', ext_options), @@ -307,9 +312,6 @@ exts_list = [ ('jsonlite', '0.9.16', ext_options), ('kohonen', '2.0.18', ext_options), ('base64', '1.1', ext_options), - ('registry', '0.3', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), ('doRNG', '1.6', ext_options), ('nleqslv', '2.8', ext_options), ('RGCCA', '2.0', ext_options), -- GitLab From bb5969ead81c891446748fc4b0cf38091001e1f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:18:13 +0200 Subject: [PATCH 922/992] add gridBase, move up doParallel --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 646fb4f5a1..413d380137 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -226,6 +226,8 @@ exts_list = [ ('registry', '0.3', ext_options), ('pkgmaker', '0.22', ext_options), ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.8', ext_options), + ('gridBase', '0.4-7', ext_options), ('NMF', '0.20.6', ext_options), ('irlba', '1.0.3', ext_options), ('igraph', '1.0.1', ext_options), @@ -340,7 +342,6 @@ exts_list = [ ('pracma', '1.8.3', ext_options), ('RCurl', '1.95-4.7', ext_options), ('bio3d', '2.2-2', ext_options), - ('doParallel', '1.0.8', ext_options), ('interpretR', '0.2.3', ext_options), ] -- GitLab From 666cf6905a7dfa95766de03025cf08511f51b92f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:28:32 +0200 Subject: [PATCH 923/992] add jsonlite --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 413d380137..2cb1e9b537 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -240,6 +240,7 @@ exts_list = [ ('ROCR', '1.0-7', ext_options), ('httpuv', '1.3.2', ext_options), ('R6', '2.1.0', ext_options), + ('jsonlite', '0.9.16', ext_options), ('shiny', '0.12.1', ext_options), ('adegenet', '2.0.0', ext_options), ('phylobase', '0.6.8', ext_options), -- GitLab From aa767358b1103742d8e0ea15f3102c37be96fb5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:46:16 +0200 Subject: [PATCH 924/992] add adegenet deps --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 2cb1e9b537..85720a0c5d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -242,6 +242,11 @@ exts_list = [ ('R6', '2.1.0', ext_options), ('jsonlite', '0.9.16', ext_options), ('shiny', '0.12.1', ext_options), + ('seqinr', '3.1-3', ext_options), + ('spdep', '0.5-88', ext_options), + ('assertthat', '0.4.2', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.2', ext_options), ('adegenet', '2.0.0', ext_options), ('phylobase', '0.6.8', ext_options), ('adephylo', '1.1-6', ext_options), -- GitLab From d403b56c642ab75fe52df69101e5e1faf7ff7fd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:48:49 +0200 Subject: [PATCH 925/992] fix assertthat version --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 85720a0c5d..f37c4bc47d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -244,7 +244,7 @@ exts_list = [ ('shiny', '0.12.1', ext_options), ('seqinr', '3.1-3', ext_options), ('spdep', '0.5-88', ext_options), - ('assertthat', '0.4.2', ext_options), + ('assertthat', '0.1', ext_options), ('lazyeval', '0.1.10', ext_options), ('dplyr', '0.4.2', ext_options), ('adegenet', '2.0.0', ext_options), -- GitLab From 7649c009f38c35f6d04708575594aa54dd7cf7c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 01:52:41 +0200 Subject: [PATCH 926/992] add spdep deps --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index f37c4bc47d..51322416bd 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -243,6 +243,8 @@ exts_list = [ ('jsonlite', '0.9.16', ext_options), ('shiny', '0.12.1', ext_options), ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), ('spdep', '0.5-88', ext_options), ('assertthat', '0.1', ext_options), ('lazyeval', '0.1.10', ext_options), -- GitLab From 59bdc78453640062a6f54af024e7e770329cb574 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 02:23:19 +0200 Subject: [PATCH 927/992] add rgl ext --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 51322416bd..1f1123a8c7 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -268,6 +268,7 @@ exts_list = [ ('fossil', '0.3.7', ext_options), ('geiger', '2.0.3', ext_options), ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1247', ext_options), ('labdsv', '1.7-0', ext_options), ('MatrixModels', '0.4-0', ext_options), ('stabs', '0.5-1', ext_options), -- GitLab From 21a9f81921a5c0f34790f2f9cdf816c476ffa3ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 02:31:50 +0200 Subject: [PATCH 928/992] add yaml --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 1f1123a8c7..46cbd47517 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -290,6 +290,7 @@ exts_list = [ ('chemometrics', '1.3.9', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), ('knitr', '1.10.5', ext_options), ('statmod', '1.4.21', ext_options), ('miscTools', '0.6-16', ext_options), -- GitLab From aaf7ec0d7712fb2cf216366c40d4a35291407b66 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 02:39:25 +0200 Subject: [PATCH 929/992] drop samr, since it depens on Bioconductor --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 46cbd47517..492d9b5716 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -307,7 +307,6 @@ exts_list = [ ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), ('matrixStats', '0.14.2', ext_options), - ('samr', '2.0', ext_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), -- GitLab From aa89237a9e040e0e693692e0e504d4ed883eb75e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 07:19:32 +0200 Subject: [PATCH 930/992] add car/flashClust deps for FactoMineR --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 492d9b5716..196ee6a36f 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -310,6 +310,10 @@ exts_list = [ ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), + ('car', '2.0-25', ext_options), + ('lme4', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('flashClust', '1.01-2', ext_options), ('FactoMineR', '1.31.3', ext_options), ('modeltools', '0.2-21', ext_options), ('flexclust', '1.3-4', ext_options), -- GitLab From a48170785308288724b5f686cd8fed1f9e0c96a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 07:27:47 +0200 Subject: [PATCH 931/992] fix order --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 196ee6a36f..7dabbdcc65 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -310,9 +310,9 @@ exts_list = [ ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), - ('car', '2.0-25', ext_options), ('lme4', '1.1-8', ext_options), ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), ('flashClust', '1.01-2', ext_options), ('FactoMineR', '1.31.3', ext_options), ('modeltools', '0.2-21', ext_options), -- GitLab From 6330576b2372a02447342082e8625e096f3b9b08 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 07:39:47 +0200 Subject: [PATCH 932/992] add nloptr --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 7dabbdcc65..041f63b861 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -310,6 +310,7 @@ exts_list = [ ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), ('lme4', '1.1-8', ext_options), ('pbkrtest', '0.4-2', ext_options), ('car', '2.0-25', ext_options), -- GitLab From 0f9fb3ba09d9586218b5b8e2607e56278ff51b20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 08:39:30 +0200 Subject: [PATCH 933/992] fix name for R-bundle-pbd easyconfig --- ...-3.1.3-pbd.eb => R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/r/R-bundle-pbd/{R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb => R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb} (100%) diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb similarity index 100% rename from easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-20150605-intel-2015a-R-3.1.3-pbd.eb rename to easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb -- GitLab From edb6061ee8b9b196dc76f1201f9389ac29d9dc26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 09:27:46 +0200 Subject: [PATCH 934/992] add curl + deps --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 041f63b861..96599e54e5 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -344,6 +344,12 @@ exts_list = [ ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), ('XML', '3.98-1.3', ext_options), + ('testthat', '0.10.0', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('rmarkdown, '0.7', ext_options), + ('magrittr', '1.5', ext_options), + ('curl', '0.9.1', ext_options), ('httr', '1.0.0', ext_options), ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), -- GitLab From a83c33dc766682a152ef0155acb2752dda1e3782 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 09:39:58 +0200 Subject: [PATCH 935/992] fix typo --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 96599e54e5..939bd1e78d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -347,7 +347,7 @@ exts_list = [ ('testthat', '0.10.0', ext_options), ('memoise', '0.2.1', ext_options), ('crayon', '1.3.1', ext_options), - ('rmarkdown, '0.7', ext_options), + ('rmarkdown', '0.7', ext_options), ('magrittr', '1.5', ext_options), ('curl', '0.9.1', ext_options), ('httr', '1.0.0', ext_options), -- GitLab From c0f2fd75e84a1eb5539fe0e9afcda5c93d4b6212 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 09:44:08 +0200 Subject: [PATCH 936/992] fix order --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 939bd1e78d..67bf63337f 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -344,9 +344,9 @@ exts_list = [ ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), ('XML', '3.98-1.3', ext_options), + ('crayon', '1.3.1', ext_options), ('testthat', '0.10.0', ext_options), ('memoise', '0.2.1', ext_options), - ('crayon', '1.3.1', ext_options), ('rmarkdown', '0.7', ext_options), ('magrittr', '1.5', ext_options), ('curl', '0.9.1', ext_options), -- GitLab From 06470814d4182c197b08e684b02de918d089765a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 09:48:15 +0200 Subject: [PATCH 937/992] fix order, again --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 67bf63337f..3da3b71713 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -344,9 +344,9 @@ exts_list = [ ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), ('crayon', '1.3.1', ext_options), ('testthat', '0.10.0', ext_options), - ('memoise', '0.2.1', ext_options), ('rmarkdown', '0.7', ext_options), ('magrittr', '1.5', ext_options), ('curl', '0.9.1', ext_options), -- GitLab From e8a99a2087c096ed93adc8e2c1c98542756e98b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:13:25 +0200 Subject: [PATCH 938/992] add custom sanity check --- .../R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb index 002b4a69ed..dd2dee5fb4 100644 --- a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb @@ -41,4 +41,9 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} +sanity_check_paths = { + 'files': [], + 'dirs': ['EMCluster', 'pbdBASE', 'pbdDEMO', 'pbdDMAT', 'pbdMPI', 'pbdSLAP', 'pmclust'], +} + moduleclass = 'lang' -- GitLab From ccc171bf66166ca4428839498c2e6812bcda86bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:46:23 +0200 Subject: [PATCH 939/992] add stringi, move up magrittr --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 3da3b71713..fd8abad242 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -110,6 +110,8 @@ exts_list = [ ('sendmailR', '1.2-1', ext_options), ('spam', '1.0-1', ext_options), ('subplex', '1.1-6', ext_options), + ('stringi', '0.5-5', ext_options), + ('magrittr', '1.5', ext_options), ('stringr', '1.0.0', ext_options), ('evaluate', '0.7', ext_options), ('logspline', '2.1.8', ext_options), @@ -348,7 +350,6 @@ exts_list = [ ('crayon', '1.3.1', ext_options), ('testthat', '0.10.0', ext_options), ('rmarkdown', '0.7', ext_options), - ('magrittr', '1.5', ext_options), ('curl', '0.9.1', ext_options), ('httr', '1.0.0', ext_options), ('maptools', '0.8-36', ext_options), -- GitLab From b529a373011f6be328cb1c0b0898b135d39376e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:51:29 +0200 Subject: [PATCH 940/992] remove rgeos, has external dep --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index fd8abad242..20d9840616 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -358,7 +358,6 @@ exts_list = [ ('polyclip', '1.3-2', ext_options), ('goftest', '1.0-3', ext_options), ('spatstat', '1.42-2', ext_options), - ('rgeos', '0.3-11', ext_options), ('gdalUtils', '0.3.1', ext_options), ('pracma', '1.8.3', ext_options), ('RCurl', '1.95-4.7', ext_options), -- GitLab From cfed94972dc3b6c8337df17429de3781521bdc7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:56:17 +0200 Subject: [PATCH 941/992] define $CURL_INCLUDES in cURL easyconfig --- easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb index e4763fc7a1..2dbc140a53 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb @@ -21,6 +21,8 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # dependencies = [('OpenSSL', '1.0.1p')] # configopts = "--with-ssl=$EBROOTOPENSSL" +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + sanity_check_paths = { 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], 'dirs': ['lib/pkgconfig'], -- GitLab From 2d9d81315b72ef06676c77a13cfad990a7d10c76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 10:58:51 +0200 Subject: [PATCH 942/992] move R libs up to resolve dep issues --- easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb | 2 ++ easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 8 ++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb index 8a52b67eb0..f234e4353b 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb @@ -21,6 +21,8 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # dependencies = [('OpenSSL', '1.0.1p')] # configopts = "--with-ssl=$EBROOTOPENSSL" +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + sanity_check_paths = { 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 0b8d49ad4e..abc5b98de0 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -213,12 +213,12 @@ exts_list = [ ('acepack', '1.3-3.3', ext_options), ('reshape2', '1.4.1', ext_options), ('gtable', '0.1.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), ('scales', '0.2.4', ext_options), ('proto', '0.3-10', ext_options), ('ggplot2', '1.0.1', ext_options), ('Hmisc', '3.15-0', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), ('fastcluster', '1.1.16', ext_options), ('chron', '2.3-45', ext_options), ('data.table', '1.9.4', ext_options), @@ -264,6 +264,7 @@ exts_list = [ ('polspline', '1.1.9', ext_options), ('TH.data', '1.0-6', ext_options), ('multcomp', '1.4-0', ext_options), + ('gridExtra', '0.9.1', ext_options), ('rms', '4.3-0', ext_options), ('RWekajars', '3.7.12-1', ext_options), ('RWeka', '0.4-24', ext_options), @@ -273,6 +274,7 @@ exts_list = [ ('chemometrics', '1.3.9', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), ('knitr', '1.10', ext_options), ('statmod', '1.4.21', ext_options), ('miscTools', '0.6-16', ext_options), @@ -285,7 +287,6 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('locfit', '1.5-9.1', ext_options), - ('gridExtra', '0.9.1', ext_options), ('GGally', '0.5.0', ext_options), ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), @@ -333,7 +334,6 @@ exts_list = [ ('polyclip', '1.3-0', ext_options), ('goftest', '1.0-2', ext_options), ('spatstat', '1.41-1', ext_options), - ('rgeos', '0.3-8', ext_options), ('gdalUtils', '0.3.1', ext_options), ('pracma', '1.8.3', ext_options), ('RCurl', '1.95-4.7', ext_options), -- GitLab From 351750493fd1895a2e4d6725d913d5ce63abf770 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 11:04:50 +0200 Subject: [PATCH 943/992] add missing AUC ext --- easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 20d9840616..2c0d705058 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -362,6 +362,7 @@ exts_list = [ ('pracma', '1.8.3', ext_options), ('RCurl', '1.95-4.7', ext_options), ('bio3d', '2.2-2', ext_options), + ('AUC', '0.3.0', ext_options), ('interpretR', '0.2.3', ext_options), ] -- GitLab From d463c0b4200cc0c7571f64a03414d068023f90b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 11:33:05 +0200 Subject: [PATCH 944/992] {mpi}[iccifort/2015.3.187] impi 5.1.0.079 (or .038?) --- .../impi-5.1.0.038-iccifort-2015.3.187.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb new file mode 100644 index 0000000000..fb7853e6f5 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb @@ -0,0 +1,20 @@ +name = 'impi' +version = '5.1.0.079' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2015.3.187'} + +# source tarball doesn't match actual version?! +sources = ['l_mpi_p_5.1.0.038.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' -- GitLab From c3a871a3d72106546b582e802ec0cb5379ef9613 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 11:56:27 +0200 Subject: [PATCH 945/992] no mca_common_sm in OpenMPI 1.4.5 w/ ictce/5.5.0 --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index c95534677f..70d3c85032 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -26,7 +26,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], -- GitLab From aff33db32783674ae05e280613771d2288eb1647 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:03:08 +0200 Subject: [PATCH 946/992] fix easyconfig filename --- ...cifort-2015.3.187.eb => impi-5.1.0.079-iccifort-2015.3.187.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/impi/{impi-5.1.0.038-iccifort-2015.3.187.eb => impi-5.1.0.079-iccifort-2015.3.187.eb} (100%) diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb similarity index 100% rename from easybuild/easyconfigs/i/impi/impi-5.1.0.038-iccifort-2015.3.187.eb rename to easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb -- GitLab From 3797f7040c0b36f78a86a1191cfbb0db036fb4aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:33:57 +0200 Subject: [PATCH 947/992] move samr to R-bundle-Bioconductor, where it belongs --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 1 + easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 2e05c29673..27d1fa3cbd 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -112,6 +112,7 @@ exts_list = [ ('SPIA', '2.20.0', bioconductor_options), ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), + ('samr', '2.0', ext_options), # requires impute ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index abc5b98de0..809e9331c0 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -291,7 +291,6 @@ exts_list = [ ('beanplot', '1.2', ext_options), ('clValid', '0.6-6', ext_options), ('matrixStats', '0.14.0', ext_options), - ('samr', '2.0', ext_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), -- GitLab From 618b9e8cba4ad3d4afbef207d804139d1c9b032e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:35:20 +0200 Subject: [PATCH 948/992] {bio}[intel/2015a] Bioconductor 3.1 bundle for R 3.2.1 --- ...le-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 125 ++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb new file mode 100644 index 0000000000..f8eef1d152 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -0,0 +1,125 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +rver = '3.2.1' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', rver)] + +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.1', bioconductor_options), + ('IRanges', '2.2.5', bioconductor_options), + ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.1', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('BiocParallel', '1.2.9', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.3', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.13', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), + ('baySeq', '2.2.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), + ('DEGseq', '1.22.0', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), + ('NOISeq', '2.12.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), + ('BSgenome', '1.36.2', bioconductor_options), + ('VariantAnnotation', '1.14.6', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.0', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), + ('samr', '2.0', ext_options), # requires impute +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From 0717fece3bb0ab591bf32096d3499cf92c51425d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:35:51 +0200 Subject: [PATCH 949/992] change moduleclass for R-bundle-Bioconductor to 'bio' --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 27d1fa3cbd..76380a1f11 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -122,4 +122,4 @@ sanity_check_paths = { 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], } -moduleclass = 'lang' +moduleclass = 'bio' -- GitLab From e1ddeb8ade75bfda67f6d7b5d3195cc7bca48b1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 12:46:49 +0200 Subject: [PATCH 950/992] comment out Rmpi --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 809e9331c0..e180920b15 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -53,7 +53,8 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + # Rmpi segfaults (on some systems) when built with goolf/1.7.20? + #('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), ('geometry', '0.3-5', ext_options), -- GitLab From 5a6a70f9b4032f7387fe136ca6a6696551dccbcf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 13:43:10 +0200 Subject: [PATCH 951/992] include ext_options definition --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index f8eef1d152..c74f4d7cd1 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -16,6 +16,15 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [('R', rver)] +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', @@ -25,7 +34,7 @@ bioconductor_options = { 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', + 'source_tmpl': name_tmpl, } # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends -- GitLab From 4fbe0215f69860552f776419d4bea605f0edd595 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 13:43:50 +0200 Subject: [PATCH 952/992] include ext_options definition in Bioconductor easyconfig --- .../R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 76380a1f11..4d24094c6b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -16,6 +16,15 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [('R', rver)] +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', @@ -25,7 +34,7 @@ bioconductor_options = { 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', + 'source_tmpl': name_tmpl, } # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends -- GitLab From d0fbdbfb1f7864e0738eeede3c967e5173a786c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 13:52:42 +0200 Subject: [PATCH 953/992] add futile.logger dep for BiocParallel --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index c74f4d7cd1..a79c96313b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -51,6 +51,7 @@ exts_list = [ ('Biostrings', '2.36.1', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), + ('futile.logger', '1.4.1', ext_options), ('BiocParallel', '1.2.9', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), ('ShortRead', '1.26.0', bioconductor_options), -- GitLab From 2f05c60d67f6d5468253b0d50ca8c42c4ddc3d28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 14:00:30 +0200 Subject: [PATCH 954/992] add deps for futile.logger --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index a79c96313b..17cc903943 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -51,6 +51,8 @@ exts_list = [ ('Biostrings', '2.36.1', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), ('futile.logger', '1.4.1', ext_options), ('BiocParallel', '1.2.9', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), -- GitLab From 33bca956c364e1e2e7340dd5aa02bc7ac98e53b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 14:14:40 +0200 Subject: [PATCH 955/992] include perm --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 17cc903943..a93886919a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -73,6 +73,7 @@ exts_list = [ ('oligoClasses', '1.30.0', bioconductor_options), ('edgeR', '3.10.2', bioconductor_options), ('PFAM.db', '3.1.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), ('baySeq', '2.2.0', bioconductor_options), ('qvalue', '2.0.0', bioconductor_options), ('impute', '1.42.0', bioconductor_options), -- GitLab From 7cac100e34dd5ae66369ac868fc46662ae3c288a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 14:29:15 +0200 Subject: [PATCH 956/992] move up samr --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index a93886919a..062278968b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -77,6 +77,7 @@ exts_list = [ ('baySeq', '2.2.0', bioconductor_options), ('qvalue', '2.0.0', bioconductor_options), ('impute', '1.42.0', bioconductor_options), + ('samr', '2.0', ext_options), ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), -- GitLab From f392ebf6ea616c5dba2436d2a7353679e6ccc424 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:06:05 +0200 Subject: [PATCH 957/992] fix counts + long line --- RELEASE_NOTES | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index da12db80a1..bfb73bccb6 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,19 +3,30 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,689 easyconfig files, for 611 different software packages, -33 different (compiler) toolchains and 12 software bundles. +The latest version of easybuild-easyconfig provides 4,053 easyconfig files, for 673 different software packages, +34 different (compiler) toolchains, 12 software bundles and 1 meta-package. v2.2.0 (July 14th 2015) ----------------------- feature + bugfix release -- added example easyconfig files for XXX new software packages: - ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171), Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995), EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), frealign (#1619), FPM (#1440), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760), libXScrnSaver (#1653), MATIO (#1004), MuTect *#1483), ncdf (#617), NEMO (#1640), ngspice (#1116), ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412), Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776), rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658), SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot (#1100), Vampir (#512), VampirServer (#512), verifyBamID (#1675) +- added example easyconfig files for 62 new software packages: + ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171), + Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995), + EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), FPM (#1440), + frealign (#1619), g2log (#1035), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762), + GraphViz (#1658), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760), + libXScrnSaver (#1653), MATIO (#1004), MuTect (#1483), ncdf (#617), NEMO (#1640), ngspice (#1116), + ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412), + Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776), + rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658), + SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot360ex (#1100), Vampir (#512), + VampirServer (#512), verifyBamID (#1675) - added easyconfigs for 4 new software bundles: R-bundle-Bioconductor (#1573), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), R-bundle-pbd (#1659) - added easyconfigs for new GNU toolchain (#1346, #1669) - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 +- added example easyconfig for generating buildenv module (#1503) - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1, Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1 -- GitLab From 0c163b787dd72de6937da66cd422edbd36b79e54 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:08:57 +0200 Subject: [PATCH 958/992] move up GenomicFeatures --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 062278968b..4d63b897fb 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -81,6 +81,7 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), ('siggenes', '1.42.0', bioconductor_options), @@ -96,7 +97,6 @@ exts_list = [ ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), ('rtracklayer', '1.28.6', bioconductor_options), - ('GenomicFeatures', '1.20.1', bioconductor_options), ('BSgenome', '1.36.2', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), -- GitLab From c3fd5250e3fac5929e75752a1ddf5778685aaa47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:16:39 +0200 Subject: [PATCH 959/992] include #1795 --- RELEASE_NOTES | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index bfb73bccb6..fea7c3746c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -23,7 +23,8 @@ feature + bugfix release SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot360ex (#1100), Vampir (#512), VampirServer (#512), verifyBamID (#1675) - added easyconfigs for 4 new software bundles: - R-bundle-Bioconductor (#1573), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), R-bundle-pbd (#1659) + R-bundle-Bioconductor (#1573, #1795), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), + R-bundle-pbd (#1659) - added easyconfigs for new GNU toolchain (#1346, #1669) - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 - added example easyconfig for generating buildenv module (#1503) -- GitLab From b853f6a8c1796a3dc843cc33d2008cd53792a88b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:26:39 +0200 Subject: [PATCH 960/992] move up biomaRt and rtracklayer --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 4d63b897fb..e873d159b8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -81,6 +81,8 @@ exts_list = [ ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), ('GenomicFeatures', '1.20.1', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), @@ -90,13 +92,11 @@ exts_list = [ ('NOISeq', '2.12.0', bioconductor_options), ('Rgraphviz', '2.12.0', bioconductor_options), ('RNASeqPower', '1.8.0', bioconductor_options), - ('biomaRt', '2.24.0', bioconductor_options), ('annotate', '1.46.1', bioconductor_options), ('GSEABase', '1.30.2', bioconductor_options), ('genefilter', '1.50.0', bioconductor_options), ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('rtracklayer', '1.28.6', bioconductor_options), ('BSgenome', '1.36.2', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), -- GitLab From a7f1c3703c59899b86f43d9015f94975c6f29943 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 15:28:13 +0200 Subject: [PATCH 961/992] drop duplicate samr --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index e873d159b8..03f3e4ca29 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -126,7 +126,6 @@ exts_list = [ ('SPIA', '2.20.0', bioconductor_options), ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), - ('samr', '2.0', ext_options), # requires impute ] modextrapaths = {'R_LIBS': ''} -- GitLab From 162e94acb808417537a65209848ec586e8b9afef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 16:21:49 +0200 Subject: [PATCH 962/992] include GEOquery --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 03f3e4ca29..5b03ff4971 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -116,6 +116,7 @@ exts_list = [ ('KEGGREST', '1.8.0', bioconductor_options), ('KEGGgraph', '1.26.0', bioconductor_options), ('KEGGprofile', '1.10.0', bioconductor_options), + ('GEOquery', '2.34.0', bioconductor_options), ('minfi', '1.14.0', bioconductor_options), ('methylumi', '2.14.0', bioconductor_options), ('lumi', '2.20.2', bioconductor_options), -- GitLab From 60a1ef9f3066b1d0d056d31cfd93d8409aa336cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 16:29:07 +0200 Subject: [PATCH 963/992] add FDb.InfiniumMethylation.hg19 --- .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 5b03ff4971..3042f7627a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -118,6 +118,7 @@ exts_list = [ ('KEGGprofile', '1.10.0', bioconductor_options), ('GEOquery', '2.34.0', bioconductor_options), ('minfi', '1.14.0', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), ('methylumi', '2.14.0', bioconductor_options), ('lumi', '2.20.2', bioconductor_options), ('widgetTools', '1.46.0', bioconductor_options), -- GitLab From 2557dc5f9d8a0b0c5870cf09eabe430f97499d24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 16:58:10 +0200 Subject: [PATCH 964/992] add missing R pkgs --- ...bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 14 ++++++++++---- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 12 +++++++++++- 2 files changed, 21 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index 4d24094c6b..dcfb8699cb 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -51,6 +51,9 @@ exts_list = [ ('Biostrings', '2.36.1', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), ('BiocParallel', '1.2.9', bioconductor_options), ('GenomicAlignments', '1.4.1', bioconductor_options), ('ShortRead', '1.26.0', bioconductor_options), @@ -70,12 +73,17 @@ exts_list = [ ('oligoClasses', '1.30.0', bioconductor_options), ('edgeR', '3.10.2', bioconductor_options), ('PFAM.db', '3.1.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), ('baySeq', '2.2.0', bioconductor_options), ('qvalue', '2.0.0', bioconductor_options), ('impute', '1.42.0', bioconductor_options), + ('samr', '2.0', ext_options), ('DEGseq', '1.22.0', bioconductor_options), ('hgu133plus2.db', '3.1.3', bioconductor_options), ('illuminaio', '0.10.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), ('bumphunter', '1.8.0', bioconductor_options), ('multtest', '2.24.0', bioconductor_options), ('siggenes', '1.42.0', bioconductor_options), @@ -84,14 +92,11 @@ exts_list = [ ('NOISeq', '2.12.0', bioconductor_options), ('Rgraphviz', '2.12.0', bioconductor_options), ('RNASeqPower', '1.8.0', bioconductor_options), - ('biomaRt', '2.24.0', bioconductor_options), ('annotate', '1.46.1', bioconductor_options), ('GSEABase', '1.30.2', bioconductor_options), ('genefilter', '1.50.0', bioconductor_options), ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('rtracklayer', '1.28.6', bioconductor_options), - ('GenomicFeatures', '1.20.1', bioconductor_options), ('BSgenome', '1.36.2', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), @@ -111,7 +116,9 @@ exts_list = [ ('KEGGREST', '1.8.0', bioconductor_options), ('KEGGgraph', '1.26.0', bioconductor_options), ('KEGGprofile', '1.10.0', bioconductor_options), + ('GEOquery', '2.34.0', bioconductor_options), ('minfi', '1.14.0', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), ('methylumi', '2.14.0', bioconductor_options), ('lumi', '2.20.2', bioconductor_options), ('widgetTools', '1.46.0', bioconductor_options), @@ -121,7 +128,6 @@ exts_list = [ ('SPIA', '2.20.0', bioconductor_options), ('Gviz', '1.12.1', bioconductor_options), ('cummeRbund', '2.10.0', bioconductor_options), - ('samr', '2.0', ext_options), # requires impute ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index e180920b15..37f178514d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -295,6 +295,11 @@ exts_list = [ ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), + ('flashClust', '1.01-2', ext_options), ('FactoMineR', '1.29', ext_options), ('modeltools', '0.2-21', ext_options), ('flexclust', '1.3-4', ext_options), @@ -327,6 +332,12 @@ exts_list = [ ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), ('XML', '3.98-1.1', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('RCurl', '1.95-4.7', ext_options), ('httr', '0.6.1', ext_options), ('maptools', '0.8-36', ext_options), ('deldir', '0.1-9', ext_options), @@ -336,7 +347,6 @@ exts_list = [ ('spatstat', '1.41-1', ext_options), ('gdalUtils', '0.3.1', ext_options), ('pracma', '1.8.3', ext_options), - ('RCurl', '1.95-4.7', ext_options), ('bio3d', '2.2-2', ext_options), ] -- GitLab From f88cc097dbcb4dae8f955222ea5f189cf8a969e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 20:17:35 +0200 Subject: [PATCH 965/992] bump release date --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index fea7c3746c..cfe294a3e1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,7 +6,7 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 4,053 easyconfig files, for 673 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. -v2.2.0 (July 14th 2015) +v2.2.0 (July 15th 2015) ----------------------- feature + bugfix release -- GitLab From b69bfffcd363b1bccdac3a845fd9f13ce2fee00d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jul 2015 20:25:54 +0200 Subject: [PATCH 966/992] fix easyconfigs count --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index cfe294a3e1..8accdf9f3e 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 4,053 easyconfig files, for 673 different software packages, +The latest version of easybuild-easyconfig provides 4,061 easyconfig files, for 673 different software packages, 34 different (compiler) toolchains, 12 software bundles and 1 meta-package. v2.2.0 (July 15th 2015) -- GitLab From 0cd0cf1694fa8ea7003943505e93f699a7973d16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 09:06:40 +0200 Subject: [PATCH 967/992] revert #1785, patch is incomplete and causes segfaults --- .../o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 1 - .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 1 - .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 1 - .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 1 - .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 1 - .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 1 - .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 4 ---- .../OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 1 - .../easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb | 4 ---- .../OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 5 ----- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 4 ---- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb | 4 ---- .../OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 4 ---- .../OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 4 ---- .../o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 4 ---- .../o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch | 9 --------- 27 files changed, 93 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 4ed82a3c67..d88a606fa0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -20,10 +20,6 @@ dependencies = [('hwloc', '1.6')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 8196616926..b42d9a8b03 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 765b625b39..fc479108fe 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 2dafe6d37c..8b588833b0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,10 +19,6 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index b52aee2a71..168f6f9d23 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 27fe1fb0fc..933369e32b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,10 +24,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 47f67c7470..ccbc9394ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -13,7 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index d4ff682eca..ce23f55355 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -13,7 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 7bf566224c..c6b40582c8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -12,7 +12,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index ca196d7cca..2afbc4733e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -13,7 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 77911abd5d..8af372736a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -12,7 +12,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index d4c15d5bf5..2ae7377c37 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -12,7 +12,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-1.6.5-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index f23bde1400..4fc8978e4d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,10 +20,6 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 403555039f..0bb4349893 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,10 +18,6 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 7ea527459f..e9f2f244ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,10 +20,6 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 34b0c2b430..6687a0ffa0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -23,10 +23,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index dc5a005db0..10774dff41 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -12,7 +12,6 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', 'OpenMPI-%(version)s_common-cuda-lib.patch', 'OpenMPI-%(version)s-vt_cupti_events.patch', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index e03880908d..eeb7c2fe82 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index f7b63ddff5..a47fa4f0f1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index 713b0ea77b..c6c6f0c9ab 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -20,10 +20,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.9')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index 21b804f8c3..f5e9417cad 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'iccifort', 'version': '2013_sp1.4.211'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support @@ -22,10 +21,6 @@ dependencies = [('hwloc', '1.9')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 722d00ac9a..2eb439ac34 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index 97c6962989..e009a63259 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index 5f77464b2d..780c3c78ba 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -22,10 +22,6 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index d9c37cd004..ca0afea9dc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -23,10 +23,6 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb index 06ce242b8b..095d22d991 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -21,10 +21,6 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -patches = [ - 'openmpi-mca-params.conf-pre-1.8.6.patch', -] - libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch deleted file mode 100644 index 0d7989a781..0000000000 --- a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-pre-1.8.6.patch +++ /dev/null @@ -1,9 +0,0 @@ ---- opal/etc/openmpi-mca-params.conf.orig 2015-06-05 16:21:25.535727000 +0200 -+++ opal/etc/openmpi-mca-params.conf 2015-06-08 10:36:05.387902000 +0200 -@@ -56,3 +56,6 @@ - - # See "ompi_info --param all all" for a full listing of Open MPI MCA - # parameters available and their default values. -+ -+# Fix bug in the initialization of the value when using the infiniband module. (ref: http://www.open-mpi.org/community/lists/users/2015/05/26913.php) -+btl_openib_memalign_threshold=12288 -- GitLab From f1d98f4c5567db9b007e9eda833b1506b4bd0b23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 09:46:07 +0200 Subject: [PATCH 968/992] remove PR #1785 from 2.2.0 release notes (see #1798) --- RELEASE_NOTES | 1 - 1 file changed, 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 8accdf9f3e..84f7b36994 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -66,7 +66,6 @@ feature + bugfix release - remove custom exts_filter definition from Python 3.4.3 easyconfig (#1765) - fix source_urls in netCDF easyconfigs (#1766) - fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (#1767) - - add Infiniband-related patch for OpenMPI versions < 1.8.6 (#1785) v2.1.1 (May 18th 2015) ---------------------- -- GitLab From 5fae463072a3d30643290733969cb50d53b57559 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 15:10:32 +0200 Subject: [PATCH 969/992] fix typo --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 84f7b36994..7d3ae9ed16 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -49,7 +49,7 @@ feature + bugfix release - include Tcl and Tk as dependencies in R easyconfig (#1623) - add patch for installing paycheck as Py3 extension (#1629) - add Perl dependency in git 2.x easyconfigs (#1631) - - fix easycofnig for GMP 6.0.0, don't use 6.0.0a sources (#1635) + - fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources (#1635) - fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (#1652) - include Tk as dependency in Python 2.7.9 easyconfigs (#1654) - include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works (#1655) -- GitLab From 1c10dae6d02c6f7625134fb29dd5d6ce4df6abe9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 15:40:31 +0200 Subject: [PATCH 970/992] bump version to 2.3.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index d9262a0b8c..d3563514ac 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.2.0' +VERSION = '2.3.0dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From c90a030836bd3dc09eef4e82047ede30d3f09fde Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 15:40:42 +0200 Subject: [PATCH 971/992] {chem}[intel/2015a] ABINIT 7.10.4 using included deps (netCDF, libxc) --- .../ABINIT-7.10.4-intel-2015a-incl-deps.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb new file mode 100644 index 0000000000..a8aa421345 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.10.4' +versionsuffix = '-incl-deps' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bfc76a5f93c3f148c049f57541864e76'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' " +configopts += "--with-dft-flavor='atompaw+bigdft+libxc+wannier90' " +configopts += '--with-linalg-flavor=mkl --with-linalg-libs="-L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += '--enable-mpi=yes --with-mpi-level=2 --enable-mpi-io=yes ' +configopts += '--with-fft-flavor=fftw3-mkl --with-fft-libs="-L$FFT_LIB_DIR $LIBFFT" ' +configopts += '--with-fft-incs=-I$FFT_INC_DIR/fftw ' +configopts += '--enable-gw-dpc="yes" --enable-64bit-flags="yes" ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' -- GitLab From fdd766bd19ec05bce3d89153e73011cf12476e1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jul 2015 16:28:50 +0200 Subject: [PATCH 972/992] {tools}[dummy] EasyBuild 2.2.0 --- .../e/EasyBuild/EasyBuild-2.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb new file mode 100644 index 0000000000..116950af4b --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.2.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.3.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 01c6a2b26229619769c78bd49afc69f20baebc68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Jul 2015 09:13:30 +0200 Subject: [PATCH 973/992] bump version to 2.2.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index d9262a0b8c..b752afaff7 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.2.0' +VERSION = '2.2.1dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From e73ad9af2c0a1aa1ae447736f5159430109ac54f Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 27 Jul 2015 12:50:08 +0200 Subject: [PATCH 974/992] Update molmod and matplotlib for Python 2.7.9 intel 2015a. --- ...tplotlib-1.2.1-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ .../molmod-1.0-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..959081d6a0 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/matplotlib' % pythonshortversion], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..b6703cee30 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.0' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://users.ugent.be/~tovrstra/molmod'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion], +} + +moduleclass = 'math' -- GitLab From 1bb62994bcdb84401822125bfae0e9c839048e5c Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 27 Jul 2015 17:39:46 +0200 Subject: [PATCH 975/992] Update fastx-toolkit for newer intel compilers. --- .../FASTX-Toolkit-0.0.14-intel-2015a.eb | 45 +++++++++++++++++++ .../libgtextutils-0.6.1-intel-2015a.eb | 33 ++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb new file mode 100644 index 0000000000..13d9d1cb72 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +altname = name.lower().replace('-','_') +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['%s-%%(version)s.tar.bz2' % altname] + +dependencies = [('libgtextutils', '0.6.1')]; + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']], + 'dirs': ['.'] + } + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb new file mode 100644 index 0000000000..3bb784683f --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'libgtextutils' +version = '0.6.1' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] + } + +moduleclass = 'bio' -- GitLab From 18e06c15ee1de5e40b63a5313ca10070b3613750 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 29 Jul 2015 17:15:49 +0200 Subject: [PATCH 976/992] Add libraries for Python which are used for IPython notebook. --- .../p/Python/Python-2.7.10-intel-2015a.eb | 24 +++++++++++++++++++ .../p/Python/Python-2.7.9-intel-2015a.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 1977d33177..29266a2fa0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -116,6 +116,30 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + }), + ('Jinja2', '2.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('jsonpointer', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 2c04d1e9a7..8b74208902 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -114,6 +114,30 @@ exts_list = [ ('pandas', '0.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + }), + ('Jinja2', '2.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('jsonpointer', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), ] moduleclass = 'lang' -- GitLab From 18eadb23badcc94f691b6e9dce75dc45bf80adad Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 30 Jul 2015 11:59:59 +0200 Subject: [PATCH 977/992] Add Bowtie2 intel 2015a version since it's used with FASTX. --- .../b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb new file mode 100644 index 0000000000..cc4bd53b3a --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.5' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' -- GitLab From a73906b6163fbdb7ac23acb06689d02c1413a6a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Aug 2015 08:42:17 +0200 Subject: [PATCH 978/992] {tools}[dummy] GC3Pie 2.4.1 --- .../easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb new file mode 100644 index 0000000000..b62aa2387d --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.1' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.23.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From 7c12d6eb928775a4c0cd859a1a025c8cca40b370 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 5 Aug 2015 10:38:52 +0200 Subject: [PATCH 979/992] fixes for mpi enabled h5py --- .../easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index 44ec9edf7c..f4b587afd4 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -19,6 +19,9 @@ pyver = '2.7.9' pyshortver = '.'.join(pyver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pyver) +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + dependencies = [ (python, pyver), ('HDF5', '1.8.14'), -- GitLab From 9d64e69db1d24bce2bfae252ea30630e19651d4b Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 5 Aug 2015 09:42:49 +0200 Subject: [PATCH 980/992] Add molmod for Python 2.7.10 --- ...plotlib-1.2.1-intel-2015a-Python-2.7.10.eb | 35 +++++++++++++++++++ .../molmod-1.0-intel-2015a-Python-2.7.10.eb | 34 ++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..080aad8636 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..5d19338ab3 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.0' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://users.ugent.be/~tovrstra/molmod'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion], +} + +moduleclass = 'math' -- GitLab From 7c6bfa870a65392249f8918d7c183ba8f5f6e48e Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 5 Aug 2015 12:07:34 +0200 Subject: [PATCH 981/992] Whitespace changes. --- .../l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb index 3bb784683f..16d490f92b 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb @@ -18,7 +18,6 @@ version = '0.6.1' homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" - toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} @@ -26,8 +25,8 @@ sources = [SOURCE_TAR_BZ2] source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] sanity_check_paths = { - 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], - 'dirs': ['lib/pkgconfig'] - } + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} moduleclass = 'bio' -- GitLab From 23520bf3812c985129de4c52a5d31a75a9b84bce Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 5 Aug 2015 14:51:00 +0200 Subject: [PATCH 982/992] Add bowtie for intel 2015a. --- .../b/Bowtie/Bowtie-1.1.2-intel-2015a.eb | 30 +++++++++++++++++++ .../b/Bowtie/compiler-agnostic.patch | 14 +++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb new file mode 100644 index 0000000000..bbe3401bf5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb @@ -0,0 +1,30 @@ +#Modified from existing version by: +#Robert Schmidt +#Ottawa Hospital Research Institute - Bioinformatics Team +easyblock = 'MakeCp' + +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = ['compiler-agnostic.patch', 'int64typedef.patch'] + +files_to_copy = [(['bowtie', 'bowtie-build', 'bowtie-inspect'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bowtie', 'bin/bowtie-inspect'], + 'dirs': [], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch b/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch new file mode 100644 index 0000000000..a6c59b8e2f --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch @@ -0,0 +1,14 @@ +diff --git a/Makefile.orig b/Makefile +index aaccb8b..0e98c62 100644 +--- a/Makefile.orig ++++ b/Makefile +@@ -8,9 +8,6 @@ bindir = $(prefix)/bin + SEQAN_DIR = SeqAn-1.1 + SEQAN_INC = -I $(SEQAN_DIR) + INC = $(SEQAN_INC) -I third_party +-CPP = g++ +-CXX = $(CPP) +-CC = gcc + HEADERS = $(wildcard *.h) + BOWTIE_MM = 1 + BOWTIE_SHARED_MEM = 1 -- GitLab From 48d6f1e0f1fcc33308b2c3ed97515a19db3e734e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Aug 2015 10:36:14 +0200 Subject: [PATCH 983/992] {chem}[intel/2015a] libbeef 0.1.1 --- .../l/libbeef/libbeef-0.1.1-intel-2015a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb b/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb new file mode 100644 index 0000000000..d5d17f503c --- /dev/null +++ b/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libbeef' +version = '0.1.1' + +homepage = 'https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software' +description = """libbeef is a package providing the class of BEEF-vdW functionals and + Bayesian error estimates to Fortran- or C-based DFT codes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://confluence.slac.stanford.edu/download/attachments/146704476'] +sources = [SOURCE_TAR_GZ] + +configopts = 'CC="$CC"' + +sanity_check_paths = { + 'files': ['bin/bee', 'lib/libbeef.a'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From aa90db067f20dcc928e5edde782985bb09445e21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Aug 2015 10:39:26 +0200 Subject: [PATCH 984/992] bump Bioconductor 3.1 package versions --- ...R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb | 12 ++++++------ .../R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb index dcfb8699cb..cfe8ae2e84 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -42,13 +42,13 @@ bioconductor_options = { exts_list = [ ('BiocGenerics', '0.14.0', bioconductor_options), ('Biobase', '2.28.0', bioconductor_options), - ('S4Vectors', '0.6.1', bioconductor_options), + ('S4Vectors', '0.6.3', bioconductor_options), ('IRanges', '2.2.5', bioconductor_options), ('GenomeInfoDb', '1.4.1', bioconductor_options), ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.1', bioconductor_options), + ('Biostrings', '2.36.2', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), ('lambda.r', '1.1.7', ext_options), @@ -59,11 +59,11 @@ exts_list = [ ('ShortRead', '1.26.0', bioconductor_options), ('graph', '1.46.0', bioconductor_options), ('affyio', '1.36.0', bioconductor_options), - ('BiocInstaller', '1.18.3', bioconductor_options), + ('BiocInstaller', '1.18.4', bioconductor_options), ('preprocessCore', '1.30.0', bioconductor_options), ('affy', '1.46.1', bioconductor_options), ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.13', bioconductor_options), + ('limma', '3.24.14', bioconductor_options), ('RBGL', '1.44.0', bioconductor_options), ('org.Hs.eg.db', '3.1.2', bioconductor_options), ('AnnotationForge', '1.10.1', bioconductor_options), @@ -97,11 +97,11 @@ exts_list = [ ('genefilter', '1.50.0', bioconductor_options), ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('BSgenome', '1.36.2', bioconductor_options), + ('BSgenome', '1.36.3', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), - ('ggbio', '1.16.0', bioconductor_options), + ('ggbio', '1.16.1', bioconductor_options), ('geneplotter', '1.46.0', bioconductor_options), ('DESeq2', '1.8.1', bioconductor_options), ('ReportingTools', '2.8.0', bioconductor_options), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb index 3042f7627a..1f51e42d01 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -42,13 +42,13 @@ bioconductor_options = { exts_list = [ ('BiocGenerics', '0.14.0', bioconductor_options), ('Biobase', '2.28.0', bioconductor_options), - ('S4Vectors', '0.6.1', bioconductor_options), + ('S4Vectors', '0.6.3', bioconductor_options), ('IRanges', '2.2.5', bioconductor_options), ('GenomeInfoDb', '1.4.1', bioconductor_options), ('AnnotationDbi', '1.30.1', bioconductor_options), ('XVector', '0.8.0', bioconductor_options), ('zlibbioc', '1.14.0', bioconductor_options), - ('Biostrings', '2.36.1', bioconductor_options), + ('Biostrings', '2.36.2', bioconductor_options), ('GenomicRanges', '1.20.5', bioconductor_options), ('Rsamtools', '1.20.4', bioconductor_options), ('lambda.r', '1.1.7', ext_options), @@ -59,11 +59,11 @@ exts_list = [ ('ShortRead', '1.26.0', bioconductor_options), ('graph', '1.46.0', bioconductor_options), ('affyio', '1.36.0', bioconductor_options), - ('BiocInstaller', '1.18.3', bioconductor_options), + ('BiocInstaller', '1.18.4', bioconductor_options), ('preprocessCore', '1.30.0', bioconductor_options), ('affy', '1.46.1', bioconductor_options), ('GO.db', '3.1.2', bioconductor_options), - ('limma', '3.24.13', bioconductor_options), + ('limma', '3.24.14', bioconductor_options), ('RBGL', '1.44.0', bioconductor_options), ('org.Hs.eg.db', '3.1.2', bioconductor_options), ('AnnotationForge', '1.10.1', bioconductor_options), @@ -97,11 +97,11 @@ exts_list = [ ('genefilter', '1.50.0', bioconductor_options), ('Category', '2.34.2', bioconductor_options), ('GOstats', '2.34.0', bioconductor_options), - ('BSgenome', '1.36.2', bioconductor_options), + ('BSgenome', '1.36.3', bioconductor_options), ('VariantAnnotation', '1.14.6', bioconductor_options), ('biovizBase', '1.16.0', bioconductor_options), ('OrganismDbi', '1.10.0', bioconductor_options), - ('ggbio', '1.16.0', bioconductor_options), + ('ggbio', '1.16.1', bioconductor_options), ('geneplotter', '1.46.0', bioconductor_options), ('DESeq2', '1.8.1', bioconductor_options), ('ReportingTools', '2.8.0', bioconductor_options), -- GitLab From 14915716988c7a898528eccc9e5eeb575fe69374 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 6 Aug 2015 10:48:25 +0200 Subject: [PATCH 985/992] Use buildopts instead of patching the makefile. --- .../b/Bowtie/Bowtie-1.1.2-intel-2015a.eb | 4 +++- .../easyconfigs/b/Bowtie/compiler-agnostic.patch | 14 -------------- 2 files changed, 3 insertions(+), 15 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb index bbe3401bf5..c3c415f11f 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb @@ -17,7 +17,9 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://download.sourceforge.net/bowtie-bio/'] -patches = ['compiler-agnostic.patch', 'int64typedef.patch'] +patches = ['int64typedef.patch'] + +buildopts = 'CC="$CC" CXX="$CXX" CPP="$CXX"' files_to_copy = [(['bowtie', 'bowtie-build', 'bowtie-inspect'], 'bin')] diff --git a/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch b/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch deleted file mode 100644 index a6c59b8e2f..0000000000 --- a/easybuild/easyconfigs/b/Bowtie/compiler-agnostic.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff --git a/Makefile.orig b/Makefile -index aaccb8b..0e98c62 100644 ---- a/Makefile.orig -+++ b/Makefile -@@ -8,9 +8,6 @@ bindir = $(prefix)/bin - SEQAN_DIR = SeqAn-1.1 - SEQAN_INC = -I $(SEQAN_DIR) - INC = $(SEQAN_INC) -I third_party --CPP = g++ --CXX = $(CPP) --CC = gcc - HEADERS = $(wildcard *.h) - BOWTIE_MM = 1 - BOWTIE_SHARED_MEM = 1 -- GitLab From e5218465e93a8777b7d9d532b79cf7848ce12e42 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 6 Aug 2015 12:12:50 +0200 Subject: [PATCH 986/992] Remove change from 2.7.9 and add it to the foss version. --- .../p/Python/Python-2.7.10-foss-2015a.eb | 24 +++++++++++++++++++ .../p/Python/Python-2.7.9-intel-2015a.eb | 24 ------------------- 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index aa976378fe..466c60183d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -116,6 +116,30 @@ exts_list = [ ('pandas', '0.16.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + }), + ('Jinja2', '2.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('jsonpointer', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 8b74208902..2c04d1e9a7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -114,30 +114,6 @@ exts_list = [ ('pandas', '0.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], }), - ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], - }), - ('Jinja2', '2.7.3', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], - }), - ('jsonpointer', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], - }), - ('jsonschema', '2.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], - }), - ('functools32', '3.2.3-1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], - }), - ('mistune', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], - }), - ('tornado', '4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], - }), - ('Pygments', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], - }), ] moduleclass = 'lang' -- GitLab From 1e3d5ae4324d43c05bca0c8ba595b16a8f8400c8 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 6 Aug 2015 15:14:37 +0200 Subject: [PATCH 987/992] Update versions on @boegel's request. --- .../easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 12 ++++++------ .../p/Python/Python-2.7.10-intel-2015a.eb | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 466c60183d..1d7d341095 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -119,22 +119,22 @@ exts_list = [ ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], }), - ('Jinja2', '2.7.3', { + ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], }), - ('jsonpointer', '1.7', { + ('jsonpointer', '1.9', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], }), - ('jsonschema', '2.4.0', { + ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], }), - ('functools32', '3.2.3-1', { + ('functools32', '3.2.3-2', { 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], }), - ('mistune', '0.5.1', { + ('mistune', '0.7', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], }), - ('tornado', '4.1', { + ('tornado', '4.2.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], }), ('Pygments', '2.0.2', { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 29266a2fa0..a808b9876c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -119,22 +119,22 @@ exts_list = [ ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], }), - ('Jinja2', '2.7.3', { + ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], }), - ('jsonpointer', '1.7', { + ('jsonpointer', '1.9', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], }), - ('jsonschema', '2.4.0', { + ('jsonschema', '2.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], }), - ('functools32', '3.2.3-1', { + ('functools32', '3.2.3-2', { 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], }), - ('mistune', '0.5.1', { + ('mistune', '0.7', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], }), - ('tornado', '4.1', { + ('tornado', '4.2.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], }), ('Pygments', '2.0.2', { -- GitLab From 8d2631610549866bbb93896893fb7b96cd1cae1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Aug 2015 15:50:34 +0200 Subject: [PATCH 988/992] style fixes in PCRE and XZ easyconfigs --- .../p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb | 8 ++++---- easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb | 8 ++++---- easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb | 8 ++++---- easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb | 9 ++++----- easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb | 10 ++++------ easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb | 10 ++++------ easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb | 6 ++---- easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb | 10 ++++------ easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb | 7 ++++--- easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb | 7 ++++--- easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb | 7 ++++--- easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb | 5 ++++- 12 files changed, 46 insertions(+), 49 deletions(-) diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb index e95902eec8..4a9ef5925f 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5.""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb index 0f58883e8e..5916d698fc 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax -and semantics as Perl 5.""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb index ae806687ed..e5f29eb85e 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5.""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb index 0a2a528704..871d373c07 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb @@ -4,16 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5.""" - +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb index 82e14a704f..365ae1e42a 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """ - The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5. -""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb index fd30422f0b..a4df16eaad 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.35' homepage = 'http://www.pcre.org/' -description = """ - The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5. -""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb index dd7d330b7c..7881c04da4 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb @@ -4,10 +4,8 @@ name = 'PCRE' version = '8.36' homepage = 'http://www.pcre.org/' -description = """ - The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5. -""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb index 64ff0ffd54..f2529df084 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.36' homepage = 'http://www.pcre.org/' -description = """ - The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5. -""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb index fad6a95d95..3d54b29efd 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'GCC', 'version': '4.8.2'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'GCC', 'version': '4.8.2'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb index 171e02c46b..e60568da6e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb index c7b1752259..6f7148a406 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'ictce', 'version': '5.3.0'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb index 5a6ed9b122..99b4d29f28 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb @@ -6,10 +6,13 @@ version = '5.2.0' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'GCC', 'version': '4.9.2'} +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], -- GitLab From fd12b56c77004c7adf0d0e3f6a088ee94b74c264 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Aug 2015 23:52:15 +0200 Subject: [PATCH 989/992] {tools}[dummy] GC3Pie 2.4.2 --- .../easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb new file mode 100644 index 0000000000..e73e2257cc --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.2' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.23.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' -- GitLab From 5a45e61862b71a718c6f16aff446dc00b04ad50b Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 7 Aug 2015 10:03:08 +0200 Subject: [PATCH 990/992] correct import of fancylogger --- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/suite.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9ccac83960..68fd8a7c50 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -36,7 +36,7 @@ import shutil import sys import tempfile from distutils.version import LooseVersion -from vsc import fancylogger +from vsc.utils import fancylogger from vsc.utils.missing import nub from unittest import TestCase, TestLoader, main diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 65497da038..6afbd6ffb1 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -36,7 +36,8 @@ import shutil import sys import tempfile import unittest -from vsc import fancylogger + +from vsc.utils import fancylogger import easybuild.tools.build_log # initialize EasyBuild logging, so we disable it import test.easyconfigs.easyconfigs as e -- GitLab From ca880b15a9fcf87db803cf8b1a15d8baf162e585 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 00:20:04 +0200 Subject: [PATCH 991/992] put dummy template values in place to make comparison with dumped easyconfig more robust --- .../easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb | 2 +- .../easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 2 +- test/easyconfigs/easyconfigs.py | 8 ++++++++ 4 files changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb index 0e1e6d0fb4..67920d1a2d 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o FastTree')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb index 5fb2a1352d..b7b0c00339 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o FastTree')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 50633eb598..7bcbad6706 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -30,7 +30,7 @@ dependencies = [('ZPAQ', '7.00')] skipsteps = ['source'] cmds_map = [ - ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %(source)s $EBROOTZPAQ/include/libzpaq.cpp -o fastqz'), + ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %(source)s $EBROOTZPAQ/include/libzpaq.cpp -o %(name)s'), ('fapack.cpp', '$CXX $CFLAGS -s %(source)s -o %(target)s') ] diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 68fd8a7c50..a8b8f5a2f2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -311,6 +311,14 @@ def template_easyconfig_test(self, spec): dumped_ec = EasyConfig(test_ecfile) os.remove(test_ecfile) + # inject dummy values for templates that are only known at a later stage + dummy_template_values = { + 'builddir': '/dummy/builddir', + 'installdir': '/dummy/installdir', + } + ec.template_values.update(dummy_template_values) + dumped_ec.template_values.update(dummy_template_values) + for key in sorted(ec._config): self.assertEqual(ec[key], dumped_ec[key]) -- GitLab From c424d2f5195b43e1e60b33f25295a9f895f6847a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Aug 2015 21:28:51 +0200 Subject: [PATCH 992/992] {compiler}[dummy] GCC 5.2.0 --- easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb | 49 + .../GCC/mpfr-3.1.3-allpatches-20150717.patch | 1699 +++++++++++++++++ 2 files changed, 1748 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb new file mode 100644 index 0000000000..c25b63f7b1 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -0,0 +1,49 @@ +name = 'GCC' +version = '5.2.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.3' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20150717.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [('M4', '1.4.17')] + +checksums = [ + 'a51bcfeb3da7dd4c623e27207ed43467', # gcc-5.2.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.l.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + 'e502185ebb22b41c528f183bb22a7569', # mpfr-3.1.3-allpatches-20150717.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch new file mode 100644 index 0000000000..7793316052 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch @@ -0,0 +1,1699 @@ +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:49:23.950112879 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:49:24.042113845 +0000 +@@ -0,0 +1 @@ ++lngamma-and-doc +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-06-19 19:55:09.000000000 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:49:24.042113845 +0000 +@@ -1 +1 @@ +-3.1.3 ++3.1.3-p1 +diff -Naurd mpfr-3.1.3-a/doc/mpfr.texi mpfr-3.1.3-b/doc/mpfr.texi +--- mpfr-3.1.3-a/doc/mpfr.texi 2015-06-19 19:55:11.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.texi 2015-07-02 10:49:24.018113593 +0000 +@@ -810,13 +810,17 @@ + When the input point is in the closure of the domain of the mathematical + function and an input argument is +0 (resp.@: @minus{}0), one considers + the limit when the corresponding argument approaches 0 from above +-(resp.@: below). If the limit is not defined (e.g., @code{mpfr_log} on +-@minus{}0), the behavior is specified in the description of the MPFR function. ++(resp.@: below), if possible. If the limit is not defined (e.g., ++@code{mpfr_sqrt} and @code{mpfr_log} on @minus{}0), the behavior is ++specified in the description of the MPFR function, but must be consistent ++with the rule from the above paragraph (e.g., @code{mpfr_log} on @pom{}0 ++gives @minus{}Inf). + + When the result is equal to 0, its sign is determined by considering the + limit as if the input point were not in the domain: If one approaches 0 + from above (resp.@: below), the result is +0 (resp.@: @minus{}0); +-for example, @code{mpfr_sin} on +0 gives +0. ++for example, @code{mpfr_sin} on @minus{}0 gives @minus{}0 and ++@code{mpfr_acos} on 1 gives +0 (in all rounding modes). + In the other cases, the sign is specified in the description of the MPFR + function; for example @code{mpfr_max} on @minus{}0 and +0 gives +0. + +@@ -832,8 +836,8 @@ + @c that advantages in practice), like for any bug fix. + Example: @code{mpfr_hypot} on (NaN,0) gives NaN, but @code{mpfr_hypot} + on (NaN,+Inf) gives +Inf (as specified in @ref{Special Functions}), +-since for any finite input @var{x}, @code{mpfr_hypot} on (@var{x},+Inf) +-gives +Inf. ++since for any finite or infinite input @var{x}, @code{mpfr_hypot} on ++(@var{x},+Inf) gives +Inf. + + @node Exceptions, Memory Handling, Floating-Point Values on Special Numbers, MPFR Basics + @comment node-name, next, previous, up +@@ -1581,7 +1585,8 @@ + @deftypefunx int mpfr_add_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_add_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} + @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) + 0 = (+0) and (@minus{}0) + 0 = (@minus{}0)). + The @code{mpfr_add_d} function assumes that the radix of the @code{double} type + is a power of 2, with a precision at most that declared by the C implementation +@@ -1599,7 +1604,8 @@ + @deftypefunx int mpfr_sub_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sub_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} - @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) @minus{} 0 = (+0), (@minus{}0) @minus{} 0 = (@minus{}0), + 0 @minus{} (+0) = (@minus{}0) and 0 @minus{} (@minus{}0) = (+0)). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_sub} +@@ -1615,7 +1621,7 @@ + Set @var{rop} to @math{@var{op1} @GMPtimes{} @var{op2}} rounded in the + direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_mul_d}. + @end deftypefun + +@@ -1635,7 +1641,7 @@ + @deftypefunx int mpfr_div_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1}/@var{op2}} rounded in the direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_div} + and @code{mpfr_div_d}. + @end deftypefun +@@ -1643,15 +1649,18 @@ + @deftypefun int mpfr_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sqrt_ui (mpfr_t @var{rop}, unsigned long int @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{\sqrt{@var{op}}, the square root of @var{op}} +-rounded in the direction @var{rnd} (set @var{rop} to @minus{}0 if @var{op} is +-@minus{}0, to be consistent with the IEEE 754 standard). ++rounded in the direction @var{rnd}. Set @var{rop} to @minus{}0 if ++@var{op} is @minus{}0, to be consistent with the IEEE 754 standard. + Set @var{rop} to NaN if @var{op} is negative. + @end deftypefun + + @deftypefun int mpfr_rec_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{1/\sqrt{@var{op}}, the reciprocal square root of @var{op}} +-rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is +-@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. ++rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is ++@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. Warning! ++Therefore the result on @minus{}0 is different from the one of the rSqrt ++function recommended by the IEEE 754-2008 standard (Section 9.2.1), which ++is @minus{}Inf instead of +Inf. + @end deftypefun + + @deftypefun int mpfr_cbrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -1832,7 +1841,9 @@ + @m{\log_2 @var{op}, log2(@var{op})} or + @m{\log_{10} @var{op}, log10(@var{op})}, respectively, + rounded in the direction @var{rnd}. +-Set @var{rop} to @minus{}Inf if @var{op} is @minus{}0 ++Set @var{rop} to +0 if @var{op} is 1 (in all rounding modes), ++for consistency with the ISO C99 and IEEE 754-2008 standards. ++Set @var{rop} to @minus{}Inf if @var{op} is @pom{}0 + (i.e., the sign of the zero has no influence on the result). + @end deftypefun + +@@ -2003,8 +2014,11 @@ + @deftypefun int mpfr_lngamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to the value of the logarithm of the Gamma function on @var{op}, + rounded in the direction @var{rnd}. +-When @math{@minus{}2@var{k}@minus{}1 @le{} @var{op} @le{} @minus{}2@var{k}}, +-@var{k} being a non-negative integer, @var{rop} is set to NaN. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf, ++following the general rules on special values. ++When @math{@minus{}2@var{k}@minus{}1 < @var{op} < @minus{}2@var{k}}, ++@var{k} being a nonnegative integer, set @var{rop} to NaN@. + See also @code{mpfr_lgamma}. + @end deftypefun + +@@ -2012,10 +2026,11 @@ + Set @var{rop} to the value of the logarithm of the absolute value of the + Gamma function on @var{op}, rounded in the direction @var{rnd}. The sign + (1 or @minus{}1) of Gamma(@var{op}) is returned in the object pointed to +-by @var{signp}. When @var{op} is an infinity or a non-positive integer, set +-@var{rop} to +Inf. When @var{op} is NaN, @minus{}Inf or a negative integer, +-*@var{signp} is undefined, and when @var{op} is @pom{}0, *@var{signp} is +-the sign of the zero. ++by @var{signp}. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf. ++When @var{op} is NaN, @minus{}Inf or a negative integer, *@var{signp} is ++undefined, and when @var{op} is @pom{}0, *@var{signp} is the sign of the zero. + @end deftypefun + + @deftypefun int mpfr_digamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -2064,7 +2079,10 @@ + @deftypefunx int mpfr_fms (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_t @var{op3}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{(@var{op1} @GMPtimes{} @var{op2}) + @var{op3}} + (resp.@: @math{(@var{op1} @GMPtimes{} @var{op2}) - @var{op3}}) +-rounded in the direction @var{rnd}. ++rounded in the direction @var{rnd}. Concerning special values (signed zeros, ++infinities, NaN), these functions behave like a multiplication followed by a ++separate addition or subtraction. That is, the fused operation matters only ++for rounding. + @end deftypefun + + @deftypefun int mpfr_agm (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_rnd_t @var{rnd}) +@@ -2089,8 +2107,8 @@ + i.e., $\sqrt{x^2+y^2}$, + @end tex + rounded in the direction @var{rnd}. +-Special values are handled as described in Section F.9.4.3 of +-the ISO C99 and IEEE 754-2008 standards: ++Special values are handled as described in the ISO C99 (Section F.9.4.3) ++and IEEE 754-2008 (Section 9.2.1) standards: + If @var{x} or @var{y} is an infinity, then +Inf is returned in @var{rop}, + even if the other number is NaN. + @end deftypefun +diff -Naurd mpfr-3.1.3-a/doc/mpfr.info mpfr-3.1.3-b/doc/mpfr.info +--- mpfr-3.1.3-a/doc/mpfr.info 2015-06-19 19:55:53.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.info 2015-07-02 10:49:38.718267817 +0000 +@@ -1,4 +1,4 @@ +-This is mpfr.info, produced by makeinfo version 5.2 from mpfr.texi. ++This is mpfr.info, produced by makeinfo version 6.0 from mpfr.texi. + + This manual documents how to install and use the Multiple Precision + Floating-Point Reliable Library, version 3.1.3. +@@ -55,7 +55,7 @@ + MPFR Copying Conditions + *********************** + +-The GNU MPFR library (or MPFR for short) is "free"; this means that ++The GNU MPFR library (or MPFR for short) is “free”; this means that + everyone is free to use it and free to redistribute it on a free basis. + The library is not in the public domain; it is copyrighted and there are + restrictions on its distribution, but these restrictions are designed to +@@ -418,7 +418,7 @@ + 4.2 Nomenclature and Types + ========================== + +-A "floating-point number", or "float" for short, is an arbitrary ++A “floating-point number”, or “float” for short, is an arbitrary + precision significand (also called mantissa) with a limited precision + exponent. The C data type for such objects is ‘mpfr_t’ (internally + defined as a one-element array of a structure, and ‘mpfr_ptr’ is the C +@@ -432,7 +432,7 @@ + to the other functions supported by MPFR. Unless documented otherwise, + the sign bit of a NaN is unspecified. + +-The "precision" is the number of bits used to represent the significand ++The “precision” is the number of bits used to represent the significand + of a floating-point number; the corresponding C data type is + ‘mpfr_prec_t’. The precision can be any integer between ‘MPFR_PREC_MIN’ + and ‘MPFR_PREC_MAX’. In the current implementation, ‘MPFR_PREC_MIN’ is +@@ -446,7 +446,7 @@ + may abort, crash or have undefined behavior (depending on your C + implementation). + +-The "rounding mode" specifies the way to round the result of a ++The “rounding mode” specifies the way to round the result of a + floating-point operation, in case the exact result can not be + represented exactly in the destination significand; the corresponding C + data type is ‘mpfr_rnd_t’. +@@ -499,14 +499,14 @@ + representable numbers, it is rounded to the one with the least + significant bit set to zero. For example, the number 2.5, which is + represented by (10.1) in binary, is rounded to (10.0)=2 with a precision +-of two bits, and not to (11.0)=3. This rule avoids the "drift" ++of two bits, and not to (11.0)=3. This rule avoids the “drift” + phenomenon mentioned by Knuth in volume 2 of The Art of Computer + Programming (Section 4.2.2). + + Most MPFR functions take as first argument the destination variable, + as second and following arguments the input variables, as last argument + a rounding mode, and have a return value of type ‘int’, called the +-"ternary value". The value stored in the destination variable is ++“ternary value”. The value stored in the destination variable is + correctly rounded, i.e., MPFR behaves as if it computed the result with + an infinite precision, then rounded it to the precision of this + variable. The input variables are regarded as exact (in particular, +@@ -572,15 +572,18 @@ + When the input point is in the closure of the domain of the + mathematical function and an input argument is +0 (resp. −0), one + considers the limit when the corresponding argument approaches 0 from +-above (resp. below). If the limit is not defined (e.g., ‘mpfr_log’ on +-−0), the behavior is specified in the description of the MPFR function. ++above (resp. below), if possible. If the limit is not defined (e.g., ++‘mpfr_sqrt’ and ‘mpfr_log’ on −0), the behavior is specified in the ++description of the MPFR function, but must be consistent with the rule ++from the above paragraph (e.g., ‘mpfr_log’ on ±0 gives −Inf). + + When the result is equal to 0, its sign is determined by considering + the limit as if the input point were not in the domain: If one + approaches 0 from above (resp. below), the result is +0 (resp. −0); for +-example, ‘mpfr_sin’ on +0 gives +0. In the other cases, the sign is +-specified in the description of the MPFR function; for example +-‘mpfr_max’ on −0 and +0 gives +0. ++example, ‘mpfr_sin’ on −0 gives −0 and ‘mpfr_acos’ on 1 gives +0 (in all ++rounding modes). In the other cases, the sign is specified in the ++description of the MPFR function; for example ‘mpfr_max’ on −0 and +0 ++gives +0. + + When the input point is not in the closure of the domain of the + function, the result is NaN. Example: ‘mpfr_sqrt’ on −17 gives NaN. +@@ -590,8 +593,8 @@ + numbers; such a case is always explicitly specified in *note MPFR + Interface::. Example: ‘mpfr_hypot’ on (NaN,0) gives NaN, but + ‘mpfr_hypot’ on (NaN,+Inf) gives +Inf (as specified in *note Special +-Functions::), since for any finite input X, ‘mpfr_hypot’ on (X,+Inf) +-gives +Inf. ++Functions::), since for any finite or infinite input X, ‘mpfr_hypot’ on ++(X,+Inf) gives +Inf. + +  + File: mpfr.info, Node: Exceptions, Next: Memory Handling, Prev: Floating-Point Values on Special Numbers, Up: MPFR Basics +@@ -1253,8 +1256,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_add_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 + OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) + 0 = ++ Set ROP to OP1 + OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) + 0 = + (+0) and (−0) + 0 = (−0)). The ‘mpfr_add_d’ function assumes that + the radix of the ‘double’ type is a power of 2, with a precision at + most that declared by the C implementation (macro +@@ -1280,8 +1284,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_sub_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 - OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) − 0 = ++ Set ROP to OP1 - OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) − 0 = + (+0), (−0) − 0 = (−0), 0 − (+0) = (−0) and 0 − (−0) = (+0)). The + same restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_sub’ and + ‘mpfr_sub_d’. +@@ -1300,7 +1305,7 @@ + mpfr_rnd_t RND) + Set ROP to OP1 times OP2 rounded in the direction RND. When a + result is zero, its sign is the product of the signs of the +- operands (for types having no signed zero, it is considered ++ operands (for types having no signed zeros, 0 is considered + positive). The same restrictions than for ‘mpfr_add_d’ apply to + ‘mpfr_mul_d’. + +@@ -1327,21 +1332,24 @@ + mpfr_rnd_t RND) + Set ROP to OP1/OP2 rounded in the direction RND. When a result is + zero, its sign is the product of the signs of the operands (for +- types having no signed zero, it is considered positive). The same ++ types having no signed zeros, 0 is considered positive). The same + restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_div’ and + ‘mpfr_div_d’. + + -- Function: int mpfr_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_sqrt_ui (mpfr_t ROP, unsigned long int OP, + mpfr_rnd_t RND) +- Set ROP to the square root of OP rounded in the direction RND (set +- ROP to −0 if OP is −0, to be consistent with the IEEE 754 +- standard). Set ROP to NaN if OP is negative. ++ Set ROP to the square root of OP rounded in the direction RND. Set ++ ROP to −0 if OP is −0, to be consistent with the IEEE 754 standard. ++ Set ROP to NaN if OP is negative. + + -- Function: int mpfr_rec_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the reciprocal square root of OP rounded in the + direction RND. Set ROP to +Inf if OP is ±0, +0 if OP is +Inf, and +- NaN if OP is negative. ++ NaN if OP is negative. Warning! Therefore the result on −0 is ++ different from the one of the rSqrt function recommended by the ++ IEEE 754-2008 standard (Section 9.2.1), which is −Inf instead of ++ +Inf. + + -- Function: int mpfr_cbrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_root (mpfr_t ROP, mpfr_t OP, unsigned long int K, +@@ -1515,8 +1523,10 @@ + -- Function: int mpfr_log2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_log10 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the natural logarithm of OP, log2(OP) or log10(OP), +- respectively, rounded in the direction RND. Set ROP to −Inf if OP +- is −0 (i.e., the sign of the zero has no influence on the result). ++ respectively, rounded in the direction RND. Set ROP to +0 if OP is ++ 1 (in all rounding modes), for consistency with the ISO C99 and ++ IEEE 754-2008 standards. Set ROP to −Inf if OP is ±0 (i.e., the ++ sign of the zero has no influence on the result). + + -- Function: int mpfr_exp (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_exp2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) +@@ -1649,17 +1659,21 @@ + + -- Function: int mpfr_lngamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the Gamma function on OP, +- rounded in the direction RND. When −2K−1 <= OP <= −2K, K being a +- non-negative integer, ROP is set to NaN. See also ‘mpfr_lgamma’. ++ rounded in the direction RND. When OP is 1 or 2, set ROP to +0 (in ++ all rounding modes). When OP is an infinity or a nonpositive ++ integer, set ROP to +Inf, following the general rules on special ++ values. When −2K−1 < OP < −2K, K being a nonnegative integer, set ++ ROP to NaN. See also ‘mpfr_lgamma’. + + -- Function: int mpfr_lgamma (mpfr_t ROP, int *SIGNP, mpfr_t OP, + mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the absolute value of the + Gamma function on OP, rounded in the direction RND. The sign (1 or + −1) of Gamma(OP) is returned in the object pointed to by SIGNP. +- When OP is an infinity or a non-positive integer, set ROP to +Inf. +- When OP is NaN, −Inf or a negative integer, *SIGNP is undefined, +- and when OP is ±0, *SIGNP is the sign of the zero. ++ When OP is 1 or 2, set ROP to +0 (in all rounding modes). When OP ++ is an infinity or a nonpositive integer, set ROP to +Inf. When OP ++ is NaN, −Inf or a negative integer, *SIGNP is undefined, and when ++ OP is ±0, *SIGNP is the sign of the zero. + + -- Function: int mpfr_digamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the Digamma (sometimes also called Psi) +@@ -1703,7 +1717,10 @@ + -- Function: int mpfr_fms (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, mpfr_t + OP3, mpfr_rnd_t RND) + Set ROP to (OP1 times OP2) + OP3 (resp. (OP1 times OP2) - OP3) +- rounded in the direction RND. ++ rounded in the direction RND. Concerning special values (signed ++ zeros, infinities, NaN), these functions behave like a ++ multiplication followed by a separate addition or subtraction. ++ That is, the fused operation matters only for rounding. + + -- Function: int mpfr_agm (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, + mpfr_rnd_t RND) +@@ -1717,9 +1734,10 @@ + RND) + Set ROP to the Euclidean norm of X and Y, i.e., the square root of + the sum of the squares of X and Y, rounded in the direction RND. +- Special values are handled as described in Section F.9.4.3 of the +- ISO C99 and IEEE 754-2008 standards: If X or Y is an infinity, then +- +Inf is returned in ROP, even if the other number is NaN. ++ Special values are handled as described in the ISO C99 (Section ++ F.9.4.3) and IEEE 754-2008 (Section 9.2.1) standards: If X or Y is ++ an infinity, then +Inf is returned in ROP, even if the other number ++ is NaN. + + -- Function: int mpfr_ai (mpfr_t ROP, mpfr_t X, mpfr_rnd_t RND) + Set ROP to the value of the Airy function Ai on X, rounded in the +@@ -2670,7 +2688,7 @@ + 5.16 Internals + ============== + +-A "limb" means the part of a multi-precision number that fits in a ++A “limb” means the part of a multi-precision number that fits in a + single word. Usually a limb contains 32 or 64 bits. The C data type + for a limb is ‘mp_limb_t’. + +@@ -3140,7 +3158,7 @@ + 0. PREAMBLE + + The purpose of this License is to make a manual, textbook, or other +- functional and useful document "free" in the sense of freedom: to ++ functional and useful document “free” in the sense of freedom: to + assure everyone the effective freedom to copy and redistribute it, + with or without modifying it, either commercially or + noncommercially. Secondarily, this License preserves for the +@@ -3655,9 +3673,9 @@ + * Menu: + + * mpfr_abs: Basic Arithmetic Functions. +- (line 160) +-* mpfr_acos: Special Functions. (line 51) +-* mpfr_acosh: Special Functions. (line 115) ++ (line 165) ++* mpfr_acos: Special Functions. (line 53) ++* mpfr_acosh: Special Functions. (line 117) + * mpfr_add: Basic Arithmetic Functions. + (line 6) + * mpfr_add_d: Basic Arithmetic Functions. +@@ -3670,15 +3688,15 @@ + (line 8) + * mpfr_add_z: Basic Arithmetic Functions. + (line 14) +-* mpfr_agm: Special Functions. (line 210) +-* mpfr_ai: Special Functions. (line 226) +-* mpfr_asin: Special Functions. (line 52) +-* mpfr_asinh: Special Functions. (line 116) ++* mpfr_agm: Special Functions. (line 219) ++* mpfr_ai: Special Functions. (line 236) ++* mpfr_asin: Special Functions. (line 54) ++* mpfr_asinh: Special Functions. (line 118) + * mpfr_asprintf: Formatted Output Functions. + (line 193) +-* mpfr_atan: Special Functions. (line 53) +-* mpfr_atan2: Special Functions. (line 63) +-* mpfr_atanh: Special Functions. (line 117) ++* mpfr_atan: Special Functions. (line 55) ++* mpfr_atan2: Special Functions. (line 65) ++* mpfr_atanh: Special Functions. (line 119) + * mpfr_buildopt_decimal_p: Miscellaneous Functions. + (line 162) + * mpfr_buildopt_gmpinternals_p: Miscellaneous Functions. +@@ -3690,7 +3708,7 @@ + * mpfr_can_round: Rounding Related Functions. + (line 39) + * mpfr_cbrt: Basic Arithmetic Functions. +- (line 108) ++ (line 113) + * mpfr_ceil: Integer Related Functions. + (line 7) + * mpfr_check_range: Exception Related Functions. +@@ -3735,18 +3753,18 @@ + (line 27) + * mpfr_cmp_z: Comparison Functions. + (line 11) +-* mpfr_const_catalan: Special Functions. (line 237) +-* mpfr_const_euler: Special Functions. (line 236) +-* mpfr_const_log2: Special Functions. (line 234) +-* mpfr_const_pi: Special Functions. (line 235) ++* mpfr_const_catalan: Special Functions. (line 247) ++* mpfr_const_euler: Special Functions. (line 246) ++* mpfr_const_log2: Special Functions. (line 244) ++* mpfr_const_pi: Special Functions. (line 245) + * mpfr_copysign: Miscellaneous Functions. + (line 109) +-* mpfr_cos: Special Functions. (line 29) +-* mpfr_cosh: Special Functions. (line 95) +-* mpfr_cot: Special Functions. (line 47) +-* mpfr_coth: Special Functions. (line 111) +-* mpfr_csc: Special Functions. (line 46) +-* mpfr_csch: Special Functions. (line 110) ++* mpfr_cos: Special Functions. (line 31) ++* mpfr_cosh: Special Functions. (line 97) ++* mpfr_cot: Special Functions. (line 49) ++* mpfr_coth: Special Functions. (line 113) ++* mpfr_csc: Special Functions. (line 48) ++* mpfr_csch: Special Functions. (line 112) + * mpfr_custom_get_exp: Custom Interface. (line 75) + * mpfr_custom_get_kind: Custom Interface. (line 65) + * mpfr_custom_get_significand: Custom Interface. (line 70) +@@ -3756,47 +3774,47 @@ + * mpfr_custom_move: Custom Interface. (line 82) + * MPFR_DECL_INIT: Initialization Functions. + (line 74) +-* mpfr_digamma: Special Functions. (line 166) ++* mpfr_digamma: Special Functions. (line 172) + * mpfr_dim: Basic Arithmetic Functions. +- (line 166) ++ (line 171) + * mpfr_div: Basic Arithmetic Functions. +- (line 72) ++ (line 74) + * mpfr_divby0_p: Exception Related Functions. + (line 134) + * mpfr_div_2exp: Compatibility with MPF. + (line 49) + * mpfr_div_2si: Basic Arithmetic Functions. +- (line 181) ++ (line 186) + * mpfr_div_2ui: Basic Arithmetic Functions. +- (line 179) ++ (line 184) + * mpfr_div_d: Basic Arithmetic Functions. +- (line 84) ++ (line 86) + * mpfr_div_q: Basic Arithmetic Functions. +- (line 88) ++ (line 90) + * mpfr_div_si: Basic Arithmetic Functions. +- (line 80) ++ (line 82) + * mpfr_div_ui: Basic Arithmetic Functions. +- (line 76) ++ (line 78) + * mpfr_div_z: Basic Arithmetic Functions. +- (line 86) ++ (line 88) + * mpfr_d_div: Basic Arithmetic Functions. +- (line 82) ++ (line 84) + * mpfr_d_sub: Basic Arithmetic Functions. +- (line 35) +-* mpfr_eint: Special Functions. (line 133) ++ (line 36) ++* mpfr_eint: Special Functions. (line 135) + * mpfr_eq: Compatibility with MPF. + (line 28) + * mpfr_equal_p: Comparison Functions. + (line 59) + * mpfr_erangeflag_p: Exception Related Functions. + (line 137) +-* mpfr_erf: Special Functions. (line 177) +-* mpfr_erfc: Special Functions. (line 178) +-* mpfr_exp: Special Functions. (line 23) +-* mpfr_exp10: Special Functions. (line 25) +-* mpfr_exp2: Special Functions. (line 24) +-* mpfr_expm1: Special Functions. (line 129) +-* mpfr_fac_ui: Special Functions. (line 121) ++* mpfr_erf: Special Functions. (line 183) ++* mpfr_erfc: Special Functions. (line 184) ++* mpfr_exp: Special Functions. (line 25) ++* mpfr_exp10: Special Functions. (line 27) ++* mpfr_exp2: Special Functions. (line 26) ++* mpfr_expm1: Special Functions. (line 131) ++* mpfr_fac_ui: Special Functions. (line 123) + * mpfr_fits_intmax_p: Conversion Functions. + (line 150) + * mpfr_fits_sint_p: Conversion Functions. +@@ -3815,20 +3833,20 @@ + (line 147) + * mpfr_floor: Integer Related Functions. + (line 8) +-* mpfr_fma: Special Functions. (line 203) ++* mpfr_fma: Special Functions. (line 209) + * mpfr_fmod: Integer Related Functions. + (line 92) +-* mpfr_fms: Special Functions. (line 205) ++* mpfr_fms: Special Functions. (line 211) + * mpfr_fprintf: Formatted Output Functions. + (line 157) + * mpfr_frac: Integer Related Functions. + (line 76) +-* mpfr_free_cache: Special Functions. (line 244) ++* mpfr_free_cache: Special Functions. (line 254) + * mpfr_free_str: Conversion Functions. + (line 137) + * mpfr_frexp: Conversion Functions. + (line 45) +-* mpfr_gamma: Special Functions. (line 148) ++* mpfr_gamma: Special Functions. (line 150) + * mpfr_get_d: Conversion Functions. + (line 7) + * mpfr_get_decimal64: Conversion Functions. +@@ -3887,7 +3905,7 @@ + (line 56) + * mpfr_greater_p: Comparison Functions. + (line 55) +-* mpfr_hypot: Special Functions. (line 218) ++* mpfr_hypot: Special Functions. (line 227) + * mpfr_inexflag_p: Exception Related Functions. + (line 136) + * mpfr_inf_p: Comparison Functions. +@@ -3922,21 +3940,21 @@ + (line 31) + * mpfr_integer_p: Integer Related Functions. + (line 119) +-* mpfr_j0: Special Functions. (line 182) +-* mpfr_j1: Special Functions. (line 183) +-* mpfr_jn: Special Functions. (line 184) ++* mpfr_j0: Special Functions. (line 188) ++* mpfr_j1: Special Functions. (line 189) ++* mpfr_jn: Special Functions. (line 190) + * mpfr_lessequal_p: Comparison Functions. + (line 58) + * mpfr_lessgreater_p: Comparison Functions. + (line 64) + * mpfr_less_p: Comparison Functions. + (line 57) +-* mpfr_lgamma: Special Functions. (line 157) +-* mpfr_li2: Special Functions. (line 143) +-* mpfr_lngamma: Special Functions. (line 152) ++* mpfr_lgamma: Special Functions. (line 162) ++* mpfr_li2: Special Functions. (line 145) ++* mpfr_lngamma: Special Functions. (line 154) + * mpfr_log: Special Functions. (line 16) + * mpfr_log10: Special Functions. (line 18) +-* mpfr_log1p: Special Functions. (line 125) ++* mpfr_log1p: Special Functions. (line 127) + * mpfr_log2: Special Functions. (line 17) + * mpfr_max: Miscellaneous Functions. + (line 22) +@@ -3947,29 +3965,29 @@ + * mpfr_modf: Integer Related Functions. + (line 82) + * mpfr_mul: Basic Arithmetic Functions. +- (line 51) ++ (line 53) + * mpfr_mul_2exp: Compatibility with MPF. + (line 47) + * mpfr_mul_2si: Basic Arithmetic Functions. +- (line 174) ++ (line 179) + * mpfr_mul_2ui: Basic Arithmetic Functions. +- (line 172) ++ (line 177) + * mpfr_mul_d: Basic Arithmetic Functions. +- (line 57) ++ (line 59) + * mpfr_mul_q: Basic Arithmetic Functions. +- (line 61) ++ (line 63) + * mpfr_mul_si: Basic Arithmetic Functions. +- (line 55) ++ (line 57) + * mpfr_mul_ui: Basic Arithmetic Functions. +- (line 53) ++ (line 55) + * mpfr_mul_z: Basic Arithmetic Functions. +- (line 59) ++ (line 61) + * mpfr_nanflag_p: Exception Related Functions. + (line 135) + * mpfr_nan_p: Comparison Functions. + (line 39) + * mpfr_neg: Basic Arithmetic Functions. +- (line 159) ++ (line 164) + * mpfr_nextabove: Miscellaneous Functions. + (line 15) + * mpfr_nextbelow: Miscellaneous Functions. +@@ -3983,13 +4001,13 @@ + * mpfr_overflow_p: Exception Related Functions. + (line 133) + * mpfr_pow: Basic Arithmetic Functions. +- (line 116) ++ (line 121) + * mpfr_pow_si: Basic Arithmetic Functions. +- (line 120) ++ (line 125) + * mpfr_pow_ui: Basic Arithmetic Functions. +- (line 118) ++ (line 123) + * mpfr_pow_z: Basic Arithmetic Functions. +- (line 122) ++ (line 127) + * mpfr_prec_round: Rounding Related Functions. + (line 13) + * ‘mpfr_prec_t’: Nomenclature and Types. +@@ -3999,7 +4017,7 @@ + * mpfr_print_rnd_mode: Rounding Related Functions. + (line 71) + * mpfr_rec_sqrt: Basic Arithmetic Functions. +- (line 103) ++ (line 105) + * mpfr_regular_p: Comparison Functions. + (line 43) + * mpfr_reldiff: Compatibility with MPF. +@@ -4021,11 +4039,11 @@ + * ‘mpfr_rnd_t’: Nomenclature and Types. + (line 34) + * mpfr_root: Basic Arithmetic Functions. +- (line 109) ++ (line 114) + * mpfr_round: Integer Related Functions. + (line 9) +-* mpfr_sec: Special Functions. (line 45) +-* mpfr_sech: Special Functions. (line 109) ++* mpfr_sec: Special Functions. (line 47) ++* mpfr_sech: Special Functions. (line 111) + * mpfr_set: Assignment Functions. + (line 9) + * mpfr_setsign: Miscellaneous Functions. +@@ -4100,57 +4118,57 @@ + (line 49) + * mpfr_signbit: Miscellaneous Functions. + (line 99) +-* mpfr_sin: Special Functions. (line 30) +-* mpfr_sinh: Special Functions. (line 96) +-* mpfr_sinh_cosh: Special Functions. (line 101) +-* mpfr_sin_cos: Special Functions. (line 35) ++* mpfr_sin: Special Functions. (line 32) ++* mpfr_sinh: Special Functions. (line 98) ++* mpfr_sinh_cosh: Special Functions. (line 103) ++* mpfr_sin_cos: Special Functions. (line 37) + * mpfr_si_div: Basic Arithmetic Functions. +- (line 78) ++ (line 80) + * mpfr_si_sub: Basic Arithmetic Functions. +- (line 31) ++ (line 32) + * mpfr_snprintf: Formatted Output Functions. + (line 180) + * mpfr_sprintf: Formatted Output Functions. + (line 170) + * mpfr_sqr: Basic Arithmetic Functions. +- (line 69) ++ (line 71) + * mpfr_sqrt: Basic Arithmetic Functions. +- (line 96) ++ (line 98) + * mpfr_sqrt_ui: Basic Arithmetic Functions. +- (line 97) ++ (line 99) + * mpfr_strtofr: Assignment Functions. + (line 80) + * mpfr_sub: Basic Arithmetic Functions. +- (line 25) ++ (line 26) + * mpfr_subnormalize: Exception Related Functions. + (line 60) + * mpfr_sub_d: Basic Arithmetic Functions. +- (line 37) ++ (line 38) + * mpfr_sub_q: Basic Arithmetic Functions. +- (line 43) ++ (line 44) + * mpfr_sub_si: Basic Arithmetic Functions. +- (line 33) ++ (line 34) + * mpfr_sub_ui: Basic Arithmetic Functions. +- (line 29) ++ (line 30) + * mpfr_sub_z: Basic Arithmetic Functions. +- (line 41) +-* mpfr_sum: Special Functions. (line 252) ++ (line 42) ++* mpfr_sum: Special Functions. (line 262) + * mpfr_swap: Assignment Functions. + (line 150) + * ‘mpfr_t’: Nomenclature and Types. + (line 6) +-* mpfr_tan: Special Functions. (line 31) +-* mpfr_tanh: Special Functions. (line 97) ++* mpfr_tan: Special Functions. (line 33) ++* mpfr_tanh: Special Functions. (line 99) + * mpfr_trunc: Integer Related Functions. + (line 10) + * mpfr_ui_div: Basic Arithmetic Functions. +- (line 74) ++ (line 76) + * mpfr_ui_pow: Basic Arithmetic Functions. +- (line 126) ++ (line 131) + * mpfr_ui_pow_ui: Basic Arithmetic Functions. +- (line 124) ++ (line 129) + * mpfr_ui_sub: Basic Arithmetic Functions. +- (line 27) ++ (line 28) + * mpfr_underflow_p: Exception Related Functions. + (line 132) + * mpfr_unordered_p: Comparison Functions. +@@ -4181,61 +4199,61 @@ + (line 182) + * mpfr_vsprintf: Formatted Output Functions. + (line 171) +-* mpfr_y0: Special Functions. (line 193) +-* mpfr_y1: Special Functions. (line 194) +-* mpfr_yn: Special Functions. (line 195) ++* mpfr_y0: Special Functions. (line 199) ++* mpfr_y1: Special Functions. (line 200) ++* mpfr_yn: Special Functions. (line 201) + * mpfr_zero_p: Comparison Functions. + (line 42) +-* mpfr_zeta: Special Functions. (line 171) +-* mpfr_zeta_ui: Special Functions. (line 172) ++* mpfr_zeta: Special Functions. (line 177) ++* mpfr_zeta_ui: Special Functions. (line 178) + * mpfr_z_sub: Basic Arithmetic Functions. +- (line 39) ++ (line 40) + + +  + Tag Table: + Node: Top775 + Node: Copying2007 +-Node: Introduction to MPFR3766 +-Node: Installing MPFR5880 +-Node: Reporting Bugs11323 +-Node: MPFR Basics13353 +-Node: Headers and Libraries13669 +-Node: Nomenclature and Types16828 +-Node: MPFR Variable Conventions18874 +-Node: Rounding Modes20418 +-Ref: ternary value21544 +-Node: Floating-Point Values on Special Numbers23526 +-Node: Exceptions26572 +-Node: Memory Handling29749 +-Node: MPFR Interface30894 +-Node: Initialization Functions33008 +-Node: Assignment Functions40318 +-Node: Combined Initialization and Assignment Functions49673 +-Node: Conversion Functions50974 +-Node: Basic Arithmetic Functions60035 +-Node: Comparison Functions69200 +-Node: Special Functions72687 +-Node: Input and Output Functions86672 +-Node: Formatted Output Functions88644 +-Node: Integer Related Functions98431 +-Node: Rounding Related Functions105051 +-Node: Miscellaneous Functions108888 +-Node: Exception Related Functions117568 +-Node: Compatibility with MPF124386 +-Node: Custom Interface127127 +-Node: Internals131526 +-Node: API Compatibility133066 +-Node: Type and Macro Changes134995 +-Node: Added Functions137844 +-Node: Changed Functions141132 +-Node: Removed Functions145545 +-Node: Other Changes145973 +-Node: Contributors147576 +-Node: References150219 +-Node: GNU Free Documentation License151973 +-Node: Concept Index174562 +-Node: Function and Type Index180659 ++Node: Introduction to MPFR3770 ++Node: Installing MPFR5884 ++Node: Reporting Bugs11327 ++Node: MPFR Basics13357 ++Node: Headers and Libraries13673 ++Node: Nomenclature and Types16832 ++Node: MPFR Variable Conventions18894 ++Node: Rounding Modes20438 ++Ref: ternary value21568 ++Node: Floating-Point Values on Special Numbers23554 ++Node: Exceptions26813 ++Node: Memory Handling29990 ++Node: MPFR Interface31135 ++Node: Initialization Functions33249 ++Node: Assignment Functions40559 ++Node: Combined Initialization and Assignment Functions49914 ++Node: Conversion Functions51215 ++Node: Basic Arithmetic Functions60276 ++Node: Comparison Functions69777 ++Node: Special Functions73264 ++Node: Input and Output Functions87862 ++Node: Formatted Output Functions89834 ++Node: Integer Related Functions99621 ++Node: Rounding Related Functions106241 ++Node: Miscellaneous Functions110078 ++Node: Exception Related Functions118758 ++Node: Compatibility with MPF125576 ++Node: Custom Interface128317 ++Node: Internals132716 ++Node: API Compatibility134260 ++Node: Type and Macro Changes136189 ++Node: Added Functions139038 ++Node: Changed Functions142326 ++Node: Removed Functions146739 ++Node: Other Changes147167 ++Node: Contributors148770 ++Node: References151413 ++Node: GNU Free Documentation License153167 ++Node: Concept Index175760 ++Node: Function and Type Index181857 +  + End Tag Table + +diff -Naurd mpfr-3.1.3-a/src/lngamma.c mpfr-3.1.3-b/src/lngamma.c +--- mpfr-3.1.3-a/src/lngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/lngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -603,16 +603,17 @@ + mpfr_get_prec (y), mpfr_log_prec, y, inex)); + + /* special cases */ +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x) || ++ (MPFR_IS_NEG (x) && mpfr_integer_p (x)))) + { +- if (MPFR_IS_NAN (x) || MPFR_IS_NEG (x)) ++ if (MPFR_IS_NAN (x)) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; + } +- else /* lngamma(+Inf) = lngamma(+0) = +Inf */ ++ else /* lngamma(+/-Inf) = lngamma(nonpositive integer) = +Inf */ + { +- if (MPFR_IS_ZERO (x)) ++ if (!MPFR_IS_INF (x)) + mpfr_set_divby0 (); + MPFR_SET_INF (y); + MPFR_SET_POS (y); +@@ -620,8 +621,8 @@ + } + } + +- /* if x < 0 and -2k-1 <= x <= -2k, then lngamma(x) = NaN */ +- if (MPFR_IS_NEG (x) && (unit_bit (x) == 0 || mpfr_integer_p (x))) ++ /* if -2k-1 < x < -2k <= 0, then lngamma(x) = NaN */ ++ if (MPFR_IS_NEG (x) && unit_bit (x) == 0) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3" ++#define MPFR_VERSION_STRING "3.1.3-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:49:24.042113845 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3"; ++ return "3.1.3-p1"; + } +diff -Naurd mpfr-3.1.3-a/tests/tlngamma.c mpfr-3.1.3-b/tests/tlngamma.c +--- mpfr-3.1.3-a/tests/tlngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tlngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -33,7 +33,7 @@ + special (void) + { + mpfr_t x, y; +- int inex; ++ int i, inex; + + mpfr_init (x); + mpfr_init (y); +@@ -46,25 +46,29 @@ + exit (1); + } + +- mpfr_set_inf (x, -1); ++ mpfr_set_inf (x, 1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(-Inf)\n"); ++ printf ("Error for lngamma(+Inf)\n"); + exit (1); + } + +- mpfr_set_inf (x, 1); ++ mpfr_set_inf (x, -1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(+Inf)\n"); ++ printf ("Error for lngamma(-Inf)\n"); + exit (1); + } + + mpfr_set_ui (x, 0, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(+0)\n"); + exit (1); +@@ -72,32 +76,58 @@ + + mpfr_set_ui (x, 0, MPFR_RNDN); + mpfr_neg (x, x, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(-0)\n"); + exit (1); + } + + mpfr_set_ui (x, 1, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(1)\n"); + exit (1); + } + +- mpfr_set_si (x, -1, MPFR_RNDN); +- mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ for (i = 1; i <= 5; i++) + { +- printf ("Error for lngamma(-1)\n"); +- exit (1); ++ int c; ++ ++ mpfr_set_si (x, -i, MPFR_RNDN); ++ mpfr_clear_flags (); ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) ++ { ++ printf ("Error for lngamma(-%d)\n", i); ++ exit (1); ++ } ++ if (i & 1) ++ { ++ mpfr_nextabove (x); ++ c = '+'; ++ } ++ else ++ { ++ mpfr_nextbelow (x); ++ c = '-'; ++ } ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_nan_p (y)) ++ { ++ printf ("Error for lngamma(-%d%cepsilon)\n", i, c); ++ exit (1); ++ } + } + + mpfr_set_ui (x, 2, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(2)\n"); + exit (1); +@@ -127,7 +157,7 @@ + mpfr_set_str (x, CHECK_X2, 10, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str (x, CHECK_Y2, 10, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp (y, x)) ++ if (mpfr_cmp0 (y, x)) + { + printf ("mpfr_lngamma("CHECK_X2") is wrong:\n" + "expected "); +@@ -143,7 +173,7 @@ + mpfr_lngamma (y, x, MPFR_RNDU); + mpfr_set_prec (x, 175); + mpfr_set_str_binary (x, "0.1010001100011101101011001101110010100001000001000001110011000001101100001111001001000101011011100100010101011110100111110101010100010011010010000101010111001100011000101111E7"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (1)\n"); + exit (1); +@@ -155,7 +185,7 @@ + mpfr_lngamma (x, y, MPFR_RNDZ); + mpfr_set_prec (y, 21); + mpfr_set_str_binary (y, "0.111000101000001100101E9"); +- if (MPFR_IS_NAN (x) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (120)\n"); + printf ("Expected "); mpfr_print_binary (y); puts (""); +@@ -169,7 +199,7 @@ + inex = mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 206); + mpfr_set_str_binary (x, "0.10000111011000000011100010101001100110001110000111100011000100100110110010001011011110101001111011110110000001010100111011010000000011100110110101100111000111010011110010000100010111101010001101000110101001E13"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (768)\n"); + exit (1); +@@ -185,7 +215,7 @@ + mpfr_set_str_binary (x, "0.1100E-66"); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str_binary (x, "0.1100E6"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(0.1100E-66)\n"); + exit (1); +@@ -199,7 +229,7 @@ + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 32); + mpfr_set_str_binary (x, "-0.10001000111011111011000010100010E207"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(-2^199+0.5)\n"); + printf ("Got "); +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:50:08.046573308 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:50:08.126574142 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-overflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:50:08.126574142 +0000 +@@ -1 +1 @@ +-3.1.3-p1 ++3.1.3-p2 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -49,7 +49,7 @@ + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +- else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || ++ else if (MPFR_UNLIKELY(n <= 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || + exp > __gmpfr_emax + n)) ) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 +@@ -32,7 +32,7 @@ + rnd_mode), + ("y[%Pu]=%.*Rg inexact=%d", mpfr_get_prec(y), mpfr_log_prec, y, inexact)); + +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (n == 0 || MPFR_IS_SINGULAR (x))) + return mpfr_set (y, x, rnd_mode); + else + { +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p1" ++#define MPFR_VERSION_STRING "3.1.3-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -39,7 +39,7 @@ + { + mpfr_exp_t exp = MPFR_GET_EXP (x); + MPFR_SETRAW (inexact, y, x, exp, rnd_mode); +- if (MPFR_UNLIKELY( n > 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || ++ if (MPFR_UNLIKELY(n >= 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || + exp > __gmpfr_emax - n))) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emin > MPFR_EMAX_MAX + n || +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:50:08.126574142 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p1"; ++ return "3.1.3-p2"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 +@@ -242,6 +242,76 @@ + large (MPFR_EMAX_MAX); + } + ++/* Cases where the function overflows on n = 0 when rounding is like ++ away from zero. */ ++static void ++overflow0 (mpfr_exp_t emax) ++{ ++ mpfr_exp_t old_emax; ++ mpfr_t x, y1, y2; ++ int neg, r, op; ++ static char *sop[4] = { "mul_2ui", "mul_2si", "div_2ui", "div_2si" }; ++ ++ old_emax = mpfr_get_emax (); ++ set_emax (emax); ++ ++ mpfr_init2 (x, 8); ++ mpfr_inits2 (6, y1, y2, (mpfr_ptr) 0); ++ ++ mpfr_set_inf (x, 1); ++ mpfr_nextbelow (x); ++ ++ for (neg = 0; neg <= 1; neg++) ++ { ++ RND_LOOP (r) ++ { ++ int inex1, inex2; ++ unsigned int flags1, flags2; ++ ++ /* Even if there isn't an overflow (rounding ~ toward zero), ++ the result is the same as the one of an overflow. */ ++ inex1 = mpfr_overflow (y1, (mpfr_rnd_t) r, neg ? -1 : 1); ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (mpfr_inf_p (y1)) ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ for (op = 0; op < 4; op++) ++ { ++ mpfr_clear_flags (); ++ inex2 = ++ op == 0 ? mpfr_mul_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 1 ? mpfr_mul_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 2 ? mpfr_div_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 3 ? mpfr_div_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ (MPFR_ASSERTN (0), 0); ++ flags2 = __gmpfr_flags; ++ if (!(mpfr_equal_p (y1, y2) && ++ SAME_SIGN (inex1, inex2) && ++ flags1 == flags2)) ++ { ++ printf ("Error in overflow0 for %s, mpfr_%s, emax = %" ++ MPFR_EXP_FSPEC "d,\nx = ", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r), sop[op], ++ (mpfr_eexp_t) emax); ++ mpfr_dump (x); ++ printf ("Expected "); ++ mpfr_dump (y1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (y2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } ++ mpfr_neg (x, x, MPFR_RNDN); ++ } ++ ++ mpfr_clears (x, y1, y2, (mpfr_ptr) 0); ++ set_emax (old_emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -334,6 +404,11 @@ + underflow0 (); + large0 (); + ++ if (mpfr_get_emax () != MPFR_EMAX_MAX) ++ overflow0 (mpfr_get_emax ()); ++ overflow0 (MPFR_EMAX_MAX); ++ overflow0 (-1); ++ + tests_end_mpfr (); + return 0; + } +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-17 08:54:48.592799981 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-17 08:54:48.616811495 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-underflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-17 08:54:48.616811495 +0000 +@@ -1 +1 @@ +-3.1.3-p2 ++3.1.3-p3 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -45,7 +45,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX - (n - 1) || + exp < __gmpfr_emin + (n - 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-17 08:54:48.608807656 +0000 +@@ -44,7 +44,9 @@ + if (MPFR_UNLIKELY (n >= diffexp)) /* exp - n <= emin - 1 */ + { + if (rnd_mode == MPFR_RNDN && +- (n > diffexp || (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ (n > diffexp || ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN (y)); + } +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-17 08:54:48.616811495 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p2" ++#define MPFR_VERSION_STRING "3.1.3-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -48,7 +48,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX + (n + 1) || + exp < __gmpfr_emin - (n + 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-17 08:54:48.616811495 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p2"; ++ return "3.1.3-p3"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-17 08:54:48.608807656 +0000 +@@ -50,77 +50,82 @@ + { + mpfr_t x, y, z1, z2; + mpfr_exp_t emin; +- int i, k; ++ int i, k, s; + int prec; + int rnd; + int div; + int inex1, inex2; + unsigned int flags1, flags2; + +- /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) +- * with emin = e, x = 1 + i/16, i in { -1, 0, 1 }, and k = 1 to 4, +- * by comparing the result with the one of a simple division. ++ /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) with ++ * emin = e, x = s * (1 + i/16), i in { -1, 0, 1 }, s in { -1, 1 }, and ++ * k = 1 to 4, by comparing the result with the one of a simple division. + */ + emin = mpfr_get_emin (); + set_emin (e); + mpfr_inits2 (8, x, y, (mpfr_ptr) 0); + for (i = 15; i <= 17; i++) +- { +- inex1 = mpfr_set_ui_2exp (x, i, -4, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- for (prec = 6; prec >= 3; prec -= 3) +- { +- mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); +- RND_LOOP (rnd) +- for (k = 1; k <= 4; k++) +- { +- /* The following one is assumed to be correct. */ +- inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- mpfr_clear_flags (); +- /* Do not use mpfr_div_ui to avoid the optimization +- by mpfr_div_2si. */ +- inex1 = mpfr_div (z1, y, z1, (mpfr_rnd_t) rnd); +- flags1 = __gmpfr_flags; +- +- for (div = 0; div <= 2; div++) ++ for (s = 1; s >= -1; s -= 2) ++ { ++ inex1 = mpfr_set_si_2exp (x, s * i, -4, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ for (prec = 6; prec >= 3; prec -= 3) ++ { ++ mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); ++ RND_LOOP (rnd) ++ for (k = 1; k <= 4; k++) + { ++ /* The following one is assumed to be correct. */ ++ inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); + mpfr_clear_flags (); +- inex2 = div == 0 ? +- mpfr_mul_2si (z2, x, e - k, (mpfr_rnd_t) rnd) : div == 1 ? +- mpfr_div_2si (z2, x, k - e, (mpfr_rnd_t) rnd) : +- mpfr_div_2ui (z2, x, k - e, (mpfr_rnd_t) rnd); +- flags2 = __gmpfr_flags; +- if (flags1 == flags2 && SAME_SIGN (inex1, inex2) && +- mpfr_equal_p (z1, z2)) +- continue; +- printf ("Error in underflow("); +- if (e == MPFR_EMIN_MIN) +- printf ("MPFR_EMIN_MIN"); +- else if (e == emin) +- printf ("default emin"); +- else if (e >= LONG_MIN) +- printf ("%ld", (long) e); +- else +- printf ("= LONG_MIN) ++ printf ("%ld", (long) e); ++ else ++ printf ("