From 2f660dfab2b271f3405caae4dbfc577e774915fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Dec 2013 18:54:08 +0100 Subject: [PATCH 001/701] add easyconfigs for Mono, MyMediaLite and IronPython --- .../IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb | 17 +++++++++++ .../m/Mono/Mono-2.10.6-ictce-4.1.13.eb | 30 +++++++++++++++++++ .../MyMediaLite-3.10-ictce-4.1.13.eb | 14 +++++++++ 3 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb create mode 100644 easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb new file mode 100644 index 0000000000..fb3ff7bded --- /dev/null +++ b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb @@ -0,0 +1,17 @@ +name = 'IronPython' +version = '2.7-0' +versionsuffix = '-g4fb2552' + +homepage = 'http://ironpython.net/' +description = """IronPython is an open-source implementation of the Python programming language + which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and +Python libraries, and other .NET languages can use Python code just as easily.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +# download via https://github.com/IronLanguages/main/releases +sources = ['IronLanguages-main-ipy-%(version)s%(versionsuffix)s.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb new file mode 100644 index 0000000000..05e81f5396 --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb @@ -0,0 +1,30 @@ +name = 'Mono' +version = '2.10.6' + +homepage = 'http://mono-framework.com' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +# Mono required Mono to build, so there are a couple of options: +# 1) provide Mono RPMs in sources, the Mono easyblock will use them to make a tmp Mono install +# 2) assume a Mono version is available system-wide (assert using e.g. "osdependencies = ['mono-core']") +# 3) specify an already available Mono module as build dep, e.g. "builddependencies = [('Mono', '2.10.6')] + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [ + SOURCELOWER_TAR_BZ2, + # Mono requires Mono to build, so provide RPMs so Mono can be bootstrapped + 'libgdiplus-2.4.2-2.el5.kb.x86_64.rpm', + 'mono-core-2.4.2.3-2.el5.kb.x86_64.rpm', +] + +builddependencies = [ + ('Bison', '2.6.5'), + ('gettext', '0.18.2'), +] + +parallel = 1 + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb new file mode 100644 index 0000000000..21917e5c28 --- /dev/null +++ b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-ictce-4.1.13.eb @@ -0,0 +1,14 @@ +name = 'MyMediaLite' +version = '3.10' + +homepage = 'http://www.ismll.uni-hildesheim.de/mymedialite/' +description = """MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://www.mymedialite.net/download/'] +sources = ['%(name)s-%(version)s.src.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lib' -- GitLab From d041060bb0ad8ab463dae87f32ed688975bb2f01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Mar 2014 19:55:57 +0100 Subject: [PATCH 002/701] add easyconfigs for HEALPix and CRPropa + deps --- .../c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb | 20 ++++++++++ .../c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb | 25 ++++++++++++ .../c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb | 37 ++++++++++++++++++ .../c/CRPropa/CRPropa_no-docs.patch | 11 ++++++ .../d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb | 18 +++++++++ .../h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb | 15 +++++++ .../libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb | 27 +++++++++++++ .../r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb | 39 +++++++++++++++++++ .../r/ROOT/ROOT-v5_recent-ifort.patch | 11 ++++++ 9 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5_recent-ifort.patch diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb new file mode 100644 index 0000000000..3653e27ca4 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +name = 'CFITSIO' +version = '3.350' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +srcversion = '%s' % version.replace('.', '') +source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +sanity_check_paths = { + 'files':["lib/libcfitsio.a"], + 'dirs':["include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb new file mode 100644 index 0000000000..09d2be584e --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.1.3.1' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s.tgz'] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '2.8.12')] + +# CLHEP compiles with icc instead of icpc, required out-of-source dir +srcdir = "../CLHEP" +preconfigopts = 'cd .. && mkdir obj && cd obj && export CXX="$CC" && ' +premakeopts = 'cd ../obj &&' +preinstallopts = 'cd ../obj &&' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..627472338f --- /dev/null +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb @@ -0,0 +1,37 @@ +name = 'CRPropa' +version = '2.0.3' + +homepage = 'https://crpropa.desy.de' +description = """CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron + on their voyage through an extra galactic environment.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +# download from https://github.com/CRPropa/CRPropa2 +sources = ['%(name)s%(version_major)s-%(version)s.tar.gz'] + +patches = ['CRPropa_no-docs.patch'] + +dependencies = [ + ('CLHEP', '2.1.3.1'), + ('CFITSIO', '3.350'), + ('ROOT', 'v5.34.13'), + ('FFTW', '3.3.3'), +] +builddependencies = [('Doxygen', '1.8.5')] + +configopts = '--with-clhep-path=$EBROOTCLHEP/bin' +configopts += '--with-cfitsio-include=$EBROOTCFITSIO/include --with-cfitsio-library=$EBROOTCFITSIO/lib ' +configopts += '--with-root=$EBROOTROOT/lib' + +# download and install the photo disintegration data package +premakeopts = './GetPDCrossSections.sh && ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/CRPropa"], + 'dirs': ["lib", "share"], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch b/easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch new file mode 100644 index 0000000000..f422512b07 --- /dev/null +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch @@ -0,0 +1,11 @@ +--- Makefile.in.orig 2014-03-26 17:18:53.474997093 +0100 ++++ Makefile.in 2014-03-26 17:19:18.844596386 +0100 +@@ -291,7 +291,7 @@ + AM_CPPFLAGS = $(GNL_CPPFLAGS) + + #SUBDIRS = External doc sophia dint src +-SUBDIRS = External sophia sibyll dint src doc ++SUBDIRS = External sophia sibyll dint src # doc + EXTRA_DIST = sophia/src/sophia.h sibyll/sibyll.h src/Interactions/proton_f77 src/Interactions/proton_sophia dint/src/tables sysdep.h get_externals.sh GetPDCrossSections.sh HalfLifeTable doc/Doxyfile COPYRIGHT doc/UserGuide.tex doc/precision_traj.ps doc/PhotonDensityCollection2.eps doc/crpdetector.eps doc/AllIRBzEvolutionModelsCan.eps IRBzRedshiftEvol_Kneiske examples/GettingStarted Plot + all: config.h + $(MAKE) $(AM_MAKEFLAGS) all-recursive diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb new file mode 100644 index 0000000000..e87a654b01 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.5' + +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': '5.5.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '3.0.1'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb new file mode 100644 index 0000000000..597c5e6d42 --- /dev/null +++ b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb @@ -0,0 +1,15 @@ +name = 'HEALPix' +version = '2.20a' + +homepage = 'http://healpix.sourceforge.net/' +description = """Hierarchical Equal Area isoLatitude Pixelation of a sphere.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['Healpix_%(version)s_2011Feb09.tar.gz'] + +dependencies = [('CFITSIO', '3.350')] + +moduleclass = 'math' 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 new file mode 100644 index 0000000000..ef442f4bb5 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,27 @@ +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': '5.5.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.6' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.7'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb new file mode 100644 index 0000000000..e025c77b02 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb @@ -0,0 +1,39 @@ +name = 'ROOT' +version = 'v5.34.13' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', +] + +python = 'Python' +pyver = '2.7.6' + +dependencies = [ + ('GSL', '1.16'), + ('libxml2', '2.9.1', '-%s-%s' % (python, pyver)), + (python, pyver), +] + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5_recent-ifort.patch b/easybuild/easyconfigs/r/ROOT/ROOT-v5_recent-ifort.patch new file mode 100644 index 0000000000..ad687ba67c --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5_recent-ifort.patch @@ -0,0 +1,11 @@ +--- root/config/Makefile.linuxx8664icc.orig 2013-12-02 17:22:25.630583702 +0100 ++++ root/config/Makefile.linuxx8664icc 2013-12-02 17:22:51.951053273 +0100 +@@ -87,7 +87,7 @@ + F77 = ifort + F77FLAGS = -fPIC + ifeq ($(findstring $(ICC_MAJOR),11 10 9),) +-F77LIBS := -L$(shell which ifort | sed -e 's|bin/intel64/ifort|compiler/lib|') \ ++F77LIBS := -L$(shell which ifort | sed -e 's|bin/intel64/ifort|compiler/lib/intel64|') \ + -lifcore + F77FLAGS += -m64 + else -- GitLab From e263dd04591bc6046ad0bfd26493629d45534215 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Mar 2014 20:34:25 +0100 Subject: [PATCH 003/701] add missing Bison easyconfig file --- .../b/Bison/Bison-3.0.1-ictce-5.5.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100755 easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb new file mode 100755 index 0000000000..1c5fae9cf7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +name = 'Bison' +version = '3.0.1' + +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': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files':["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs':[], +} + +moduleclass = 'lang' -- GitLab From cf4b6fd52dd38274d226e5bc84bbd2003102af15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 May 2014 13:47:04 +0200 Subject: [PATCH 004/701] add ictce easyconfig file for VCFtools --- .../p/Perl/Perl-5.16.3-ictce-5.5.0.eb | 225 ++++++++++++++++++ ...VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb | 39 +++ 2 files changed, 264 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..106bbda74e --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb @@ -0,0 +1,225 @@ +name = 'Perl' +version = '5.16.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['exitcode_error.patch'] + +runtest = 'test' + +exts_list = [ + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/IO/GAAS/'], + }), + ('Data::Stag', '0.11', { + 'source_tmpl': 'Data-Stag-0.11.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Data/CMUNGALL/'], + }), + ('DB_File', '1.827', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DB_File/PMQS/'], + }), + ('DBI', '1.625', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DBI/TIMB/'], + }), + ('Bio::Perl', '1.6.901', { + 'source_tmpl': 'BioPerl-1.6.901.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'], + 'patches': ['BioPerl_disable-broken-test.patch'], + }), + ('Sub::Uplevel', '0.24', { + 'source_tmpl': 'Sub-Uplevel-0.24.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/DAGOLDEN/'], + }), + ('Tree::DAG_Node', '1.11', { + 'source_tmpl': 'Tree-DAG_Node-1.11.tgz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Tree/RSAVAGE/'], + }), + ('Try::Tiny', '0.12', { + 'source_tmpl': 'Try-Tiny-0.12.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + }), + ('Test::Fatal', '0.010', { + 'source_tmpl': 'Test-Fatal-0.010.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/RJBS/'], + }), + ('Test::Exception', '0.31', { + 'source_tmpl': 'Test-Exception-0.31.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/ADIE/'], + }), + ('Test::Warn', '0.24', { + 'source_tmpl': 'Test-Warn-0.24.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/CHORNY/'], + }), + ('Test::Requires', '0.06', { + 'source_tmpl': 'Test-Requires-0.06.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/TOKUHIROM/'], + }), + ('Test::Tester', '0.108', { + 'source_tmpl': 'Test-Tester-0.108.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/FDALY/'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Params/ADAMK/'], + }), + ('Sub::Install', '0.926', { + 'source_tmpl': 'Sub-Install-0.926.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + }), + ('Data::OptList', '0.107', { + 'source_tmpl': 'Data-OptList-0.107.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Data/RJBS/'], + }), + ('Sub::Exporter', '0.985', { + 'source_tmpl': 'Sub-Exporter-0.985.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + }), + ('Test::Output', '1.01', { + 'source_tmpl': 'Test-Output-1.01.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/BDFOY/'], + }), + ('Module::Runtime', '0.013', { + 'source_tmpl': 'Module-Runtime-0.013.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Module/ZEFRAM/'], + }), + ('Module::Implementation', '0.06', { + 'source_tmpl': 'Module-Implementation-0.06.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Module/DROLSKY/'], + }), + ('List::MoreUtils', '0.33', { + 'source_tmpl': 'List-MoreUtils-0.33.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/List/ADAMK/'], + }), + ('Package::DeprecationManager', '0.13', { + 'source_tmpl': 'Package-DeprecationManager-0.13.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DROLSKY/'], + }), + ('Dist::CheckConflicts', '0.02', { + 'source_tmpl': 'Dist-CheckConflicts-0.02.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Dist/DOY/'], + }), + ('Package::Stash', '0.34', { + 'source_tmpl': 'Package-Stash-0.34.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DOY/'], + }), + ('Class::Load', '0.20', { + 'source_tmpl': 'Class-Load-0.20.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Class/DROLSKY/'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BO/BOBTFISH/'], + }), + ('Sub::Name', '0.05', { + 'source_tmpl': 'Sub-Name-0.05.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/FLORA/'], + }), + ('Eval::Closure', '0.08', { + 'source_tmpl': 'Eval-Closure-0.08.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + }), + ('Sub::Exporter::Progressive', '0.001010', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001010.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/FREW/'], + }), + ('Devel::GlobalDestruction', '0.11', { + 'source_tmpl': 'Devel-GlobalDestruction-0.11.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Devel/'], + }), + ('boolean', '0.30', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Tie/CHORNY/'], + }), + ('Moose', '2.0801', { + 'source_urls': ['http://www.cpan.org/modules/by-module/MooseX/ETHER/'], + }), + ('Params::Validate', '1.07', { + 'source_tmpl': 'Params-Validate-1.07.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Params/DROLSKY/'], + }), + ('DateTime::Locale', '0.45', { + 'source_tmpl': 'DateTime-Locale-0.45.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('Class::Singleton', '1.4', { + 'source_tmpl': 'Class-Singleton-1.4.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Class/ABW/'], + }), + ('DateTime::TimeZone', '1.58', { + 'source_tmpl': 'DateTime-TimeZone-1.58.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('DateTime', '1.01', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Data/DWHEELER/'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/ADAMK/'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/File/URI/'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/HTTP/GAAS/'], + }), + ('IO::HTML', '1.00', { + 'source_tmpl': 'IO-HTML-1.00.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/IO/CJM/'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/LWP/GAAS/'], + }), + ('URI', '1.60', { + 'source_urls': ['http://www.cpan.org/modules/by-module/URI/GAAS/'], + }), + ('HTTP::Request', '6.06', { + 'source_tmpl': 'HTTP-Message-6.06.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/HTTP/GAAS/'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/HTML/PETDANCE/'], + }), + ('HTML::Entities', '3.70', { + 'source_tmpl': 'HTML-Parser-3.70.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/HTML/GAAS/'], + }), + ('AnyEvent', '7.04', { + 'source_urls': ['http://www.cpan.org/modules/by-module/AnyEvent/MLEHMANN/'], + }), + ('Mouse', '1.05', { + 'source_urls': ['http://www.cpan.org/modules/by-module/MouseX/GFUJI/'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/XML/PERIGRIN/'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/XML/GRANTM/'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/XML/GRANTM/'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb new file mode 100644 index 0000000000..1350a7b674 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb @@ -0,0 +1,39 @@ +# 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 = 'VCFtools' +version = '0.1.11' + +easyblock = 'MakeCp' + +homepage = "http://vcftools.sourceforge.net/" +description = """The aim of VCFtools is to provide + methods for working with VCF files: validating, + merging, comparing and calculate some basic population + genetic statistics. """ + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) +dependencies = [ + (perl, perlver), +] + +files_to_copy = ["bin", "lib"] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 4137050e516053e1e78dd8c9c16d10744e04ecec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:47:42 +0200 Subject: [PATCH 005/701] add easyconfig for FFindex --- .../f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100755 easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb new file mode 100755 index 0000000000..3218a6e11d --- /dev/null +++ b/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +name = "FFindex" +version = "0.9.9" + +homepage = 'http://www.splashground.de/~andy/programs/FFindex/' +description = """simple index/database for huge amounts of small files""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.splashground.de/~andy/programs/FFindex/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +start_dir = 'src' + +makeopts = 'USEMPI=1' +installopts = "USEMPI=1 INSTALL_DIR=%(installdir)s" + +runtest = 'test' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ffindex_%s' % x for x in ['apply', 'build', 'from_fasta', 'get', 'modify', 'unpack']] + + ['lib64/libffindex.a', 'lib64/libffindex.so'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 12638f1690a6140bbd4fca39077f553d614ef6a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:49:14 +0200 Subject: [PATCH 006/701] add easyconfig for CFITSIO v3.300 --- .../c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100755 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb new file mode 100755 index 0000000000..06ebf30047 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +name = 'CFITSIO' +version = '3.300' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +srcversion = '%s0' % version.replace('.', '') +source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +sanity_check_paths = { + 'files':["lib/libcfitsio.a"], + 'dirs':["include"], +} + +moduleclass = 'lib' -- GitLab From 2e771de754ede797c44db85db7c763c7daaabfb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:54:07 +0200 Subject: [PATCH 007/701] add easyconfigs for log4cplus --- .../log4cplus-1.0.4.3-ictce-5.5.0.eb | 19 +++++++++++++++++++ .../log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100755 easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb create mode 100755 easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb new file mode 100755 index 0000000000..e88e8c2f72 --- /dev/null +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb @@ -0,0 +1,19 @@ +name = 'log4cplus' +version = '1.0.4.3' + +homepage = 'http://sourceforge.net/p/log4cplus' +description = """log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily +granular control over log management and configuration. It is modelled after the Java log4j API.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["lib/liblog4cplus.a", "lib/liblog4cplus.so"], + 'dirs': ["include/log4cplus"], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb new file mode 100755 index 0000000000..f5511eacf6 --- /dev/null +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb @@ -0,0 +1,19 @@ +name = 'log4cplus' +version = '1.1.2' + +homepage = 'http://sourceforge.net/p/log4cplus' +description = """log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily +granular control over log management and configuration. It is modelled after the Java log4j API.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["lib/liblog4cplus.a", "lib/liblog4cplus.so"], + 'dirs': ["include/log4cplus"], +} + +moduleclass = 'lang' -- GitLab From 0b80f86d10777c4124bb3505523540952ad8d333 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:54:54 +0200 Subject: [PATCH 008/701] add easyconfig for RDMC --- .../r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100755 easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb b/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb new file mode 100755 index 0000000000..b6cf4c64fb --- /dev/null +++ b/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb @@ -0,0 +1,22 @@ +name = 'RDMC' +version = '2.9.5' + +homepage = 'http://code.icecube.wisc.edu/' +description = "The AMANDA-era RDMC physics library" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://code.icecube.wisc.edu/tools/distfiles/%(namelower)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [('texinfo', '5.2')] + +modextrapaths = {'LD_LIBRARY_PATH': 'lib/rdmc'} + +sanity_check_paths = { + 'files': ["bin/cpfeil", "include/rdmc/rdmc.h", "include/rdmc/rdmc.inc", + "lib/rdmc/librdmc.a", "lib/rdmc/librdmc.so"], + 'dirs': [], +} + +moduleclass = 'phys' -- GitLab From 72f490ad08421b7cb0f23974841eae70d262d305 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:57:00 +0200 Subject: [PATCH 009/701] add missing texinfo easyconfig --- .../t/texinfo/texinfo-5.2-ictce-5.5.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100755 easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb new file mode 100755 index 0000000000..dc542d4583 --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb @@ -0,0 +1,18 @@ +name = 'texinfo' +version = '5.2' + +homepage = 'http://www.gnu.org/software/texinfo/' +description = "Texinfo is the official documentation format of the GNU project." + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://ftpmirror.gnu.org/texinfo'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['info', 'infokey', 'install-info', 'makeinfo', 'pdftexi2dvi', 'pod2texi', + 'texi2any', 'texi2dvi', 'texi2pdf', 'texindex']], + 'dirs': ["bin", "share"], +} + +moduleclass = 'tools' -- GitLab From 6bab96d03354a5d2bed8d5920cdfa01e028a4279 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Oct 2014 12:57:32 +0200 Subject: [PATCH 010/701] fix srcversion for CFITSIO v3.300 --- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb index 06ebf30047..e2fd327b03 100755 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb @@ -8,7 +8,7 @@ FITS (Flexible Image Transport System) data format.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} -srcversion = '%s0' % version.replace('.', '') +srcversion = version.replace('.', '') source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] -- GitLab From ef2c2773eb43f32bd3ea3702377e5ad46db01eee Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 10 Nov 2014 11:36:01 +1300 Subject: [PATCH 011/701] Use Binary easyblock --- .../i/IMOD/IMOD-4.7.12-RHEL6-64.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb new file mode 100644 index 0000000000..e39a5d8ef3 --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb @@ -0,0 +1,39 @@ +easyblock = 'Binary' + +name = 'IMOD' +version = '4.7.12_RHEL6-64' + +homepage = 'http://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'openmp': True} + +source_urls = ['http://bio3d.colorado.edu/imod/AMD64-RHEL5/'] +sources = ['%(namelower)s_%(version)s.csh'] + +install_cmd = "tcsh %(namelower)s_%(version)s.csh" + +# -dir: Choose location of installation directory +# -skip: do not attempt to deploy resource files in /etc +# -yes: do not prompt for confirmation +installopts = "-dir %(installdir)s -skip -yes" + +# The assumption by the install script is that installdir will be something +# like /usr/local. So it prefixes the install location with a lot of specific +# directories that are surplus to requirements. +postinstallcmds = ["mv %(installdir)s/%(name)s/* %(installdir)s/."] + +sanity_check_paths = { + 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'vis' + -- GitLab From fe42be6c71aeea35500030e32b81d6e3bdd3a7eb Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 10 Nov 2014 16:29:05 +1300 Subject: [PATCH 012/701] Updates to IMOD installation, including module file --- .../i/IMOD/IMOD-4.7.12-RHEL6-64.eb | 26 +++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb index e39a5d8ef3..cfe2281f3e 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb @@ -28,12 +28,34 @@ installopts = "-dir %(installdir)s -skip -yes" # The assumption by the install script is that installdir will be something # like /usr/local. So it prefixes the install location with a lot of specific # directories that are surplus to requirements. -postinstallcmds = ["mv %(installdir)s/%(name)s/* %(installdir)s/."] +postinstallcmds = [ "mv %(installdir)s/%(name)s/* %(installdir)s/.", + "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_" + ] +# "rm -r %(installdir)s/%(name)s-linux.*" sanity_check_paths = { 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], 'dirs': ['bin', 'lib'] } +# Assuming the system java /usr/java can be used. If not, we can +# cross that bridge. moduleclass = 'vis' - +modextravars = {'IMOD_DIR' : "$root", + 'IMOD_JAVADIR' : "/usr/java", + 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", + 'FOR_DISABLE_STACK_TRACE' : 1, + 'IMOD_QTLIBDIR' : "$root/qtlib"} +modaliases = {'subm' : "submfg $* &"} +modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" + +#MODULES +#------- +#include_modpath_extensions:Include $MODULEPATH extensions specified by module naming scheme. (default: True) +#modaliases: Aliases to be defined in module file (default: {}) +#modextrapaths: Extra paths to be prepended in module file (default: {}) +#modextravars: Extra environment variables to be added to module file (default: {}) +#modloadmsg: Message that should be printed when generated module is loaded (default: {}) +#modtclfooter: Footer to include in generated module file (Tcl syntax) (default: ) +#moduleforceunload: Force unload of all modules when loading the extension (default: False) +#moduleloadnoconflict: Don't check for conflicts, unload other versions instead (default: False) -- GitLab From 17cab7e752d01bb744015e90fd81ac5013023294 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Nov 2014 19:23:05 +0100 Subject: [PATCH 013/701] add easyconfig for FragGeneScan --- .../FragGeneScan-1.9-intel-2014b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb new file mode 100644 index 0000000000..807f2d8eb8 --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.19' + +homepage = 'http://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] + +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.py *.pl train example' + +files_to_copy = ['FragGeneScan', 'FGS_gff.py', 'post_process.pl', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FGS_gff.py', 'FragGeneScan', 'post_process.pl', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +moduleclass = 'bio' -- GitLab From 7d2d728ae5264cb4fa089323f558ad597235b1c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Nov 2014 20:42:57 +0100 Subject: [PATCH 014/701] fix FragGeneScan filename --- ...neScan-1.9-intel-2014b.eb => FragGeneScan-1.19-intel-2014b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/FragGeneScan/{FragGeneScan-1.9-intel-2014b.eb => FragGeneScan-1.19-intel-2014b.eb} (100%) diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.19-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.9-intel-2014b.eb rename to easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.19-intel-2014b.eb -- GitLab From 020fe80f5034e5af678bfa304b816042eaa4e937 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:09:23 +0100 Subject: [PATCH 015/701] Libint 2.0.5 for intel/2015a --- .../l/Libint/Libint-2.0.5-intel-2015a.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb new file mode 100644 index 0000000000..3e31d41c43 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -0,0 +1,14 @@ +name = 'Libint' +version = '2.0.5' + +homepage = 'https://github.com/evaleev/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': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = ['release-2-0-5.tar.gz'] +source_urls = ['https://github.com/evaleev/libint/archive/'] + +moduleclass = 'chem' -- GitLab From a408bf8a8b61d5ae228248d44d0509f670fdebb6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:15:04 +0100 Subject: [PATCH 016/701] Added autogen to libint-2.0.5 --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index 3e31d41c43..c9f9fb6f34 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} sources = ['release-2-0-5.tar.gz'] source_urls = ['https://github.com/evaleev/libint/archive/'] +preconfigopts = './autogen.sh && ' + +builddependencies = [('Autotools', '20150119', '-GCC-4.9.2')] + moduleclass = 'chem' -- GitLab From 1f135d8d0400a645b961aeff8e289822fedd649b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:17:41 +0100 Subject: [PATCH 017/701] libint: correct toolchain spec for build deps --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index c9f9fb6f34..e05864fab6 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -13,6 +13,6 @@ source_urls = ['https://github.com/evaleev/libint/archive/'] preconfigopts = './autogen.sh && ' -builddependencies = [('Autotools', '20150119', '-GCC-4.9.2')] +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] moduleclass = 'chem' -- GitLab From 75da2a27442abbd52d79f049c775485c54eb881b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:19:28 +0100 Subject: [PATCH 018/701] libint: work around incorrect permisions --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index e05864fab6..4a2c6ac340 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -11,7 +11,7 @@ toolchainopts = {'pic': True} sources = ['release-2-0-5.tar.gz'] source_urls = ['https://github.com/evaleev/libint/archive/'] -preconfigopts = './autogen.sh && ' +preconfigopts = 'sh autogen.sh && ' builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] -- GitLab From a51b7feb1d06b30aaabb930fa6210465f16978a3 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:30:56 +0100 Subject: [PATCH 019/701] Added GMP-6 for intel/2015a --- .../g/GMP/GMP-6.0.0a-intel-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb new file mode 100644 index 0000000000..b9c870dbee --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.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': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 871d1105e8bc91d8940de02e1a77f1bbaabe395d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 17:31:13 +0100 Subject: [PATCH 020/701] Libint: use new deps --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index 4a2c6ac340..b558f56bed 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -11,6 +11,11 @@ toolchainopts = {'pic': True} sources = ['release-2-0-5.tar.gz'] source_urls = ['https://github.com/evaleev/libint/archive/'] +dependencies = [ + ('GMP', '6.0.0a'), + ('Boost', '1.57.0', '-Python-2.7.9'), +] + preconfigopts = 'sh autogen.sh && ' builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] -- GitLab From eb7feca830c49a4a1700fa19740bae0ca0e8b53e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 21:05:44 +0100 Subject: [PATCH 021/701] Libint: fix remarks --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index b558f56bed..25c976800b 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libint library is used to evaluate the traditional (electron re toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} -sources = ['release-2-0-5.tar.gz'] +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] dependencies = [ @@ -16,8 +16,8 @@ dependencies = [ ('Boost', '1.57.0', '-Python-2.7.9'), ] -preconfigopts = 'sh autogen.sh && ' - builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +preconfigopts = 'sh autogen.sh && ' + moduleclass = 'chem' -- GitLab From 6da23c633530ece4f990404efa862d8e0375695b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 21:07:41 +0100 Subject: [PATCH 022/701] Libint: fix remarks part 2 --- easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb index 25c976800b..71dd5e8235 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb @@ -18,6 +18,7 @@ dependencies = [ builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +# no exec perm on the autogen.sh script preconfigopts = 'sh autogen.sh && ' moduleclass = 'chem' -- GitLab From 908e17076fd7b1d777cac4fd7da56bfa65b8a310 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 21:44:33 +0100 Subject: [PATCH 023/701] Add versionsuffix for Libint. I don't like this, but there seems to be no solution for the moment. --- ...ntel-2015a.eb => Libint-2.0.5-intel-2015a-Python-2.7.9.eb} | 4 ++++ 1 file changed, 4 insertions(+) rename easybuild/easyconfigs/l/Libint/{Libint-2.0.5-intel-2015a.eb => Libint-2.0.5-intel-2015a-Python-2.7.9.eb} (74%) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb similarity index 74% rename from easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb rename to easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index 71dd5e8235..5fecdd649f 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -1,5 +1,9 @@ name = 'Libint' version = '2.0.5' +# I'm really really not happy about this. It shouldn't be here. But PSI needs Boost-Python, +# so this also uses Boost-Python, so we add a Python suffix. This needs a better solution. +# Just to be clear: Libint doesn't need python. +versionsuffix = '-Python-2.7.9' homepage = 'https://github.com/evaleev/libint' description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body -- GitLab From c62a6922633260960144dac36e5aa83285a8b0b6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 21:54:05 +0100 Subject: [PATCH 024/701] Libint: Use versionsuffix everywhere --- .../l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index 5fecdd649f..8a3e779142 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/evaleev/libint/archive/'] dependencies = [ ('GMP', '6.0.0a'), - ('Boost', '1.57.0', '-Python-2.7.9'), + ('Boost', '1.57.0', versionsuffix), ] builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] -- GitLab From b97c3f271b1641ccbc54e0f326fb4eae22e3b906 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 22:04:01 +0100 Subject: [PATCH 025/701] Libint: less dramatic comment --- .../l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index 8a3e779142..7280d68ec2 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -1,8 +1,6 @@ name = 'Libint' version = '2.0.5' -# I'm really really not happy about this. It shouldn't be here. But PSI needs Boost-Python, -# so this also uses Boost-Python, so we add a Python suffix. This needs a better solution. -# Just to be clear: Libint doesn't need python. +# Some stuff that uses Libint (PSI) needs Boost-Python, so we inherit the versionsuffix here: #1421 versionsuffix = '-Python-2.7.9' homepage = 'https://github.com/evaleev/libint' -- GitLab From 125cf5c07cd12de0d8d87139fbf52f6e9e6c1162 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 24 Feb 2015 12:02:29 +0100 Subject: [PATCH 026/701] Let icc be more strict with fp for GMP --- easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb index b9c870dbee..83eeacce00 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb @@ -14,6 +14,7 @@ source_urls = ['http://ftp.gnu.org/gnu/gmp'] # enable C++ interface configopts = '--enable-cxx' +preconfigopts = 'CFLAGS="-O2 -xHost -ftz -fp-speculation=strict -fp-model precise" CFLAGS="$CFLAGS" ' runtest = 'check' -- GitLab From 006586a083e7fe72edd64064d1cc116e9c68243f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 24 Feb 2015 12:11:46 +0100 Subject: [PATCH 027/701] GMP: use toolchainopts --- easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb index 83eeacce00..70c2a1cb32 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb @@ -8,13 +8,13 @@ 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'} +toolchainopts = {'precise': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] # enable C++ interface configopts = '--enable-cxx' -preconfigopts = 'CFLAGS="-O2 -xHost -ftz -fp-speculation=strict -fp-model precise" CFLAGS="$CFLAGS" ' runtest = 'check' -- GitLab From a8e4451ca23a1d9d288226e61fdb81a6e2511997 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 24 Feb 2015 12:25:51 +0100 Subject: [PATCH 028/701] Libint: parrallel to 1 --- .../l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index 7280d68ec2..af61a2e991 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -23,4 +23,6 @@ builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] # no exec perm on the autogen.sh script preconfigopts = 'sh autogen.sh && ' +parallel = 1 + moduleclass = 'chem' -- GitLab From 0b7bf1c9d633097296df3711175f205c8ab27f27 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 14:42:24 +0200 Subject: [PATCH 029/701] Adding QuantumESPRESSO-5.1.2-ictce-7.3.5 --- .../QuantumESPRESSO-5.1.2-ictce-7.3.5.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb new file mode 100644 index 0000000000..a7bb611c44 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb @@ -0,0 +1,40 @@ +name = 'QuantumESPRESSO' +version = '5.1.2' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'usempi': True} + +sources = [ + 'espresso-%(version)s.tar.gz', + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.tar.gz', + 'pwcond-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + 'xspectra-%(version)s.tar.gz', + 'GWW-%(version)s.tar.gz', +] + +source_urls = [ + 'http://www.qe-forge.org/gf/download/frsrelease/185/753/', # espresso-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/752/', # atomic-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/754/', # GWW-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/755/', # PHonon-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/756/', # pwcond-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/757/', # xspectra-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/758/', # tddfpt-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/760/', # neb-5.1.2.tar.gz +] + +buildopts = 'all plumed w90 want gipaw' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' -- GitLab From d02e5a7fc948b62c7d2889e593046391932ecbb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Jun 2015 17:35:03 +0200 Subject: [PATCH 030/701] cleanup source_urls --- .../q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb index a7bb611c44..f94df6b8f2 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb @@ -22,14 +22,9 @@ sources = [ ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # others 'http://www.qe-forge.org/gf/download/frsrelease/185/753/', # espresso-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/752/', # atomic-5.1.2.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/185/754/', # GWW-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/755/', # PHonon-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/756/', # pwcond-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/757/', # xspectra-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/758/', # tddfpt-5.1.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/185/760/', # neb-5.1.2.tar.gz ] buildopts = 'all plumed w90 want gipaw' -- GitLab From e5ebd2245ea20383165b4e0052d9eb8ce8591119 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 09:51:45 +0200 Subject: [PATCH 031/701] improve comment on generic source URL --- .../q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb index f94df6b8f2..66a93062f3 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb @@ -22,7 +22,7 @@ sources = [ ] 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 and GWW*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/185/753/', # espresso-5.1.2.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/185/754/', # GWW-5.1.2.tar.gz ] -- GitLab From ad4c0ddb3dae90b7ab08f8236c17f398cf4c511a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 3 Jun 2015 10:02:45 +0200 Subject: [PATCH 032/701] use GCC GMP as intel and GMP don't get along --- .../l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb index af61a2e991..91014bdb21 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb @@ -14,7 +14,7 @@ sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] dependencies = [ - ('GMP', '6.0.0a'), + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), ('Boost', '1.57.0', versionsuffix), ] -- GitLab From 6e3352cf605895a127b60538ea57584635d1fd6e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 8 Jun 2015 11:29:16 +1200 Subject: [PATCH 033/701] Removed some unnecessary comments --- easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb index cfe2281f3e..1bf6bb89e6 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb @@ -31,7 +31,6 @@ installopts = "-dir %(installdir)s -skip -yes" postinstallcmds = [ "mv %(installdir)s/%(name)s/* %(installdir)s/.", "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_" ] -# "rm -r %(installdir)s/%(name)s-linux.*" sanity_check_paths = { 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], @@ -48,14 +47,3 @@ modextravars = {'IMOD_DIR' : "$root", 'IMOD_QTLIBDIR' : "$root/qtlib"} modaliases = {'subm' : "submfg $* &"} modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" - -#MODULES -#------- -#include_modpath_extensions:Include $MODULEPATH extensions specified by module naming scheme. (default: True) -#modaliases: Aliases to be defined in module file (default: {}) -#modextrapaths: Extra paths to be prepended in module file (default: {}) -#modextravars: Extra environment variables to be added to module file (default: {}) -#modloadmsg: Message that should be printed when generated module is loaded (default: {}) -#modtclfooter: Footer to include in generated module file (Tcl syntax) (default: ) -#moduleforceunload: Force unload of all modules when loading the extension (default: False) -#moduleloadnoconflict: Don't check for conflicts, unload other versions instead (default: False) -- GitLab From e8b5561e40f275e54b631ee27d2b79603cb844bc Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 8 Jun 2015 11:31:03 +1200 Subject: [PATCH 034/701] Renamed dash to underscore in the hope that fixes an assertion --- .../i/IMOD/{IMOD-4.7.12-RHEL6-64.eb => IMOD-4.7.12_RHEL6-64.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/IMOD/{IMOD-4.7.12-RHEL6-64.eb => IMOD-4.7.12_RHEL6-64.eb} (100%) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb similarity index 100% rename from easybuild/easyconfigs/i/IMOD/IMOD-4.7.12-RHEL6-64.eb rename to easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb -- GitLab From 767f0cd2afc2a621e7d2df61ee933c2fefdbe54c Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 8 Oct 2015 08:17:16 +1300 Subject: [PATCH 035/701] Updated configuration file for new release of IMOD 4.7 --- ....12_RHEL6-64.eb => IMOD-4.7.15_RHEL6-64_CUDA6.0.eb} | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/i/IMOD/{IMOD-4.7.12_RHEL6-64.eb => IMOD-4.7.15_RHEL6-64_CUDA6.0.eb} (86%) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb similarity index 86% rename from easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb rename to easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 1bf6bb89e6..7ada1695f6 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.12_RHEL6-64.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -1,7 +1,8 @@ easyblock = 'Binary' name = 'IMOD' -version = '4.7.12_RHEL6-64' +version = '4.7.15' +versionsuffix = '_RHEL6-64_CUDA6.0' homepage = 'http://bio3d.colorado.edu/imod/' description = """IMOD is a set of image processing, modeling and display @@ -14,11 +15,12 @@ Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" toolchain = {'name': 'dummy', 'version': 'dummy'} toolchainopts = {'openmp': True} +dependencies = [('CUDA', '6.0.37')] source_urls = ['http://bio3d.colorado.edu/imod/AMD64-RHEL5/'] -sources = ['%(namelower)s_%(version)s.csh'] +sources = ['%(namelower)s_%(version)s%(versionsuffix)s.csh'] -install_cmd = "tcsh %(namelower)s_%(version)s.csh" +install_cmd = "tcsh %(namelower)s_%(version)s%(versionsuffix)s.csh" # -dir: Choose location of installation directory # -skip: do not attempt to deploy resource files in /etc @@ -29,7 +31,7 @@ installopts = "-dir %(installdir)s -skip -yes" # like /usr/local. So it prefixes the install location with a lot of specific # directories that are surplus to requirements. postinstallcmds = [ "mv %(installdir)s/%(name)s/* %(installdir)s/.", - "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_" + "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_%(version)s" ] sanity_check_paths = { -- GitLab From 32b45df226ff531865587b3eecec0052f31aa491 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 2 Nov 2015 11:31:07 +1300 Subject: [PATCH 036/701] Reformatted --- .../i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 7ada1695f6..100020fb13 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -41,11 +41,13 @@ sanity_check_paths = { # Assuming the system java /usr/java can be used. If not, we can # cross that bridge. -moduleclass = 'vis' -modextravars = {'IMOD_DIR' : "$root", - 'IMOD_JAVADIR' : "/usr/java", - 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", - 'FOR_DISABLE_STACK_TRACE' : 1, - 'IMOD_QTLIBDIR' : "$root/qtlib"} +modextravars = { + 'IMOD_DIR' : "$root", + 'IMOD_JAVADIR' : "/usr/java", + 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", + 'FOR_DISABLE_STACK_TRACE' : 1, + 'IMOD_QTLIBDIR' : "$root/qtlib" +} modaliases = {'subm' : "submfg $* &"} modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" +moduleclass = 'vis' -- GitLab From d2838453775eea122fc9e83d88c597679979f10a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 26 Jan 2016 12:06:24 +1300 Subject: [PATCH 037/701] Add Java as a dependency --- .../i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb | 28 +++++++++++++------ 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 100020fb13..56dc7ea9cd 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -15,11 +15,18 @@ Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" toolchain = {'name': 'dummy', 'version': 'dummy'} toolchainopts = {'openmp': True} -dependencies = [('CUDA', '6.0.37')] source_urls = ['http://bio3d.colorado.edu/imod/AMD64-RHEL5/'] sources = ['%(namelower)s_%(version)s%(versionsuffix)s.csh'] +java = 'Java' +javaver = '1.8.0_40' + +dependencies = [ + ('CUDA', '6.0.37'), + (java, javaver), +] + install_cmd = "tcsh %(namelower)s_%(version)s%(versionsuffix)s.csh" # -dir: Choose location of installation directory @@ -28,26 +35,29 @@ install_cmd = "tcsh %(namelower)s_%(version)s%(versionsuffix)s.csh" installopts = "-dir %(installdir)s -skip -yes" # The assumption by the install script is that installdir will be something -# like /usr/local. So it prefixes the install location with a lot of specific -# directories that are surplus to requirements. -postinstallcmds = [ "mv %(installdir)s/%(name)s/* %(installdir)s/.", - "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_%(version)s" - ] +# like /usr/local. So it creates, within the specified install location, a +# number of additional directories within which to install IMOD. We will, +# therefore, move the contents of these directories up and throw away the +# directories themselves. Doing so apparently is not a problem so long as +# IMOD_DIR (see below) is correctly set in the module. +postinstallcmds = [ + "mv %(installdir)s/%(name)s/* %(installdir)s/.", + "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_%(version)s", +] sanity_check_paths = { 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], 'dirs': ['bin', 'lib'] } -# Assuming the system java /usr/java can be used. If not, we can -# cross that bridge. modextravars = { 'IMOD_DIR' : "$root", - 'IMOD_JAVADIR' : "/usr/java", + 'IMOD_JAVADIR' : os.getenv('EBROOTJAVA'), 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", 'FOR_DISABLE_STACK_TRACE' : 1, 'IMOD_QTLIBDIR' : "$root/qtlib" } modaliases = {'subm' : "submfg $* &"} modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" + moduleclass = 'vis' -- GitLab From 48e5277f12e469d1e17d5a779e8946242d944d8d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 Feb 2016 15:11:38 +0100 Subject: [PATCH 038/701] CP2k 3.0 for intel/2016a --- .../c/CP2K/CP2K-3.0-intel-2016a.eb | 38 +++++++++++++++++++ .../l/Libint/Libint-1.1.4-intel-2016a.eb | 24 ++++++++++++ .../l/libxc/libxc-2.2.2-intel-2016a.eb | 32 ++++++++++++++++ 3 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb new file mode 100644 index 0000000000..9d0e4f481b --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '3.0' + +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': 'intel', 'version': '2016a'} +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', '2.2.2'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# 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/l/Libint/Libint-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..61a5c02419 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.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': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'optarch': 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/libxc/libxc-2.2.2-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb new file mode 100644 index 0000000000..959f0d1356 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.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': '2016a'} +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.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From ac629d4ead19313901dfaca5df599618a24d5430 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 Feb 2016 15:12:10 +0100 Subject: [PATCH 039/701] psmp build of CP2k --- .../c/CP2K/CP2K-3.0-intel-2016a-psmp.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb new file mode 100644 index 0000000000..a3380d03a5 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb @@ -0,0 +1,42 @@ +name = 'CP2K' +version = '3.0' +versionsuffix = '-psmp' + +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': 'intel', 'version': '2016a'} +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', '2.2.2'), +# ('FFTW', '3.3.4'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +type = 'psmp' + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' -- GitLab From 42b700b5c1f404196aab8dc21c1f1159caad949e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2016 17:05:37 +0200 Subject: [PATCH 040/701] add easyconfig nco-0.0.2-intel-2016a-Python-2.7.11.eb --- .../nco-0.0.2-intel-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0732494447 --- /dev/null +++ b/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'nco' +version = '0.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nco/pynco' +description = """Python bindings for NCO""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('NCO', '4.4.9', versionsuffix), + ('numpy', '1.10.4', versionsuffix), + ('scipy', '0.16.1', versionsuffix), + ('netcdf4-python', '1.2.2', versionsuffix), + +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From 3d46bcfd86d9d374e5218083ef4f2ce80d3da28a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 2 Mar 2016 15:11:31 +1300 Subject: [PATCH 041/701] Move things into the EasyBlock --- .../i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb | 35 ------------------- 1 file changed, 35 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 56dc7ea9cd..0f356768c8 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -1,5 +1,3 @@ -easyblock = 'Binary' - name = 'IMOD' version = '4.7.15' versionsuffix = '_RHEL6-64_CUDA6.0' @@ -27,37 +25,4 @@ dependencies = [ (java, javaver), ] -install_cmd = "tcsh %(namelower)s_%(version)s%(versionsuffix)s.csh" - -# -dir: Choose location of installation directory -# -skip: do not attempt to deploy resource files in /etc -# -yes: do not prompt for confirmation -installopts = "-dir %(installdir)s -skip -yes" - -# The assumption by the install script is that installdir will be something -# like /usr/local. So it creates, within the specified install location, a -# number of additional directories within which to install IMOD. We will, -# therefore, move the contents of these directories up and throw away the -# directories themselves. Doing so apparently is not a problem so long as -# IMOD_DIR (see below) is correctly set in the module. -postinstallcmds = [ - "mv %(installdir)s/%(name)s/* %(installdir)s/.", - "rm -r %(installdir)s/%(name)s %(installdir)s/%(namelower)s_%(version)s", -] - -sanity_check_paths = { - 'files': ['IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], - 'dirs': ['bin', 'lib'] -} - -modextravars = { - 'IMOD_DIR' : "$root", - 'IMOD_JAVADIR' : os.getenv('EBROOTJAVA'), - 'IMOD_PLUGIN_DIR' : "$root/lib/imodplug", - 'FOR_DISABLE_STACK_TRACE' : 1, - 'IMOD_QTLIBDIR' : "$root/qtlib" -} -modaliases = {'subm' : "submfg $* &"} -modloadmsg = """Please set the environment variable IMOD_CALIB_DIR if appropriate.""" - moduleclass = 'vis' -- GitLab From 99d0f6d114d00a6526741abad4f07dbde9814973 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 13 Mar 2016 15:15:12 +0100 Subject: [PATCH 042/701] Update libint to 2016a and deps --- ....9.eb => Libint-2.0.5-intel-2016a-Python-2.7.11.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/l/Libint/{Libint-2.0.5-intel-2015a-Python-2.7.9.eb => Libint-2.0.5-intel-2016a-Python-2.7.11.eb} (74%) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2016a-Python-2.7.11.eb similarity index 74% rename from easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2016a-Python-2.7.11.eb index 91014bdb21..c56a331e40 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2016a-Python-2.7.11.eb @@ -1,24 +1,24 @@ name = 'Libint' version = '2.0.5' # Some stuff that uses Libint (PSI) needs Boost-Python, so we inherit the versionsuffix here: #1421 -versionsuffix = '-Python-2.7.9' +versionsuffix = '-Python-2.7.11' homepage = 'https://github.com/evaleev/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': 'intel', 'version': '2015a'} +toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] dependencies = [ - ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), - ('Boost', '1.57.0', versionsuffix), + ('GMP', '6.1.0'), + ('Boost', '1.60.0', versionsuffix), ] -builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +builddependencies = [('Autotools', '20150215')] # no exec perm on the autogen.sh script preconfigopts = 'sh autogen.sh && ' -- GitLab From 3c1b969cc8fcdeb5b03f4fc67de55c4ec7164353 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 13 Mar 2016 15:16:19 +0100 Subject: [PATCH 043/701] Drop unused GMP --- .../g/GMP/GMP-6.0.0a-intel-2015a.eb | 26 ------------------- 1 file changed, 26 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb deleted file mode 100644 index 70c2a1cb32..0000000000 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-intel-2015a.eb +++ /dev/null @@ -1,26 +0,0 @@ -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': 'intel', 'version': '2015a'} -toolchainopts = {'precise': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gmp'] - -# enable C++ interface -configopts = '--enable-cxx' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], - 'dirs': [], -} - -moduleclass = 'math' -- GitLab From 2f99209ef3e70c349dc29e7e5d417d1e1ea95000 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 13 Apr 2016 12:33:26 +0200 Subject: [PATCH 044/701] Update plumed to intel/2016a --- .../b/byacc/byacc-20160324-intel-2016a.eb | 22 ++++++++++ .../libmatheval-1.1.11-intel-2016a.eb | 33 +++++++++++++++ .../p/PLUMED/PLUMED-2.2.1-intel-2016a.eb | 42 +++++++++++++++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb b/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb new file mode 100644 index 0000000000..a80f721d5e --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20160324' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/byacc'] + +checksums = ['bde0463c6c03f059b1e6e9c5579cbe49'] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb new file mode 100644 index 0000000000..69ffa90aab --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('byacc', '20160324'), + ('guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb new file mode 100644 index 0000000000..eff628072a --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.1' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From 655557655eddce27838ed78a0fcdd2e01f947901 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 13 Apr 2016 12:40:04 +0200 Subject: [PATCH 045/701] Update CP2K to use newest PLUMED --- easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb index 9d0e4f481b..be60b5e88f 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb @@ -21,6 +21,7 @@ patches = [ dependencies = [ ('Libint', '1.1.4'), ('libxc', '2.2.2'), + ('PLUMED', '2.2.1'), ] builddependencies = [ @@ -28,6 +29,8 @@ builddependencies = [ ('Bison', '3.0.4'), ] +plumed = True + # don't use parallel make, results in compilation failure # because Fortran module files aren't created before they are needed parallel = 1 -- GitLab From b8685d0c7ed5148f294eb805515dae58af8714b9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 13 Apr 2016 17:41:43 +0200 Subject: [PATCH 046/701] Add libxsmm --- .../l/libxsmm/libxsmm-1.4-intel-2016a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb new file mode 100644 index 0000000000..e6719ce261 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.4' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/hfp/libxsmm/archive/'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' -- GitLab From 34d060379900bd4976c8d08fdcaba2b81ae33041 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 14 Apr 2016 14:53:28 +0200 Subject: [PATCH 047/701] Add libxsmm to CP2k --- easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb index be60b5e88f..a4b8c3995d 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('Libint', '1.1.4'), ('libxc', '2.2.2'), ('PLUMED', '2.2.1'), + ('libxsmm', '1.4'), ] builddependencies = [ -- GitLab From c923c1dab8db1edae7d3ee6f6351bccd59f953b3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 28 Apr 2016 16:24:03 +0800 Subject: [PATCH 048/701] {chem}[intel/2016.02-GCC-4.9] QuantumESPRESSO 5.3.0 --- ...tumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..91045a89e8 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'QuantumESPRESSO' +version = '5.3.0' + +homepage = 'http://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials.""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +source_urls = ['http://qe-forge.org/gf/download/frsrelease/204/912/'] +sources = ['espresso-%(version)s.tar.gz'] +checksums = ['6848fcfaeb118587d6be36bd10b7f2c3'] + +configopts = 'DFLAGS="-D__INTEL -D__MPI -D__PARA -D__DFTI -D__SCALAPACK" ' +configopts += 'FFT_LIBS="$LIBFFT" --with-scalapack=intel ' +configopts += '--prefix=%(installdir)s/bin' + +buildopts = 'all' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/' + prog for prog in ['average.x', 'bands.x', 'bgw2pw.x', 'cppp.x', + 'cp.x', 'd3.x', 'dist.x', 'dos.x', 'dynmat.x', 'epsilon.x', 'ev.x', 'fd_ef.x', + 'fd_ifc.x', 'fd.x', 'fqha.x', 'fs.x', 'generate_rVV10_kernel_table.x', + 'generate_vdW_kernel_table.x', 'importexport_binary.x', 'initial_state.x', + 'iotk_print_kinds.x', 'iotk.x', 'kpoints.x', 'lambda.x', 'ld1.x', + 'manypw.x', 'matdyn.x', 'molecularpdos.x', 'neb.x', 'path_interpolation.x', + 'phcg.x', 'ph.x', 'plan_avg.x', 'plotband.x', 'plotproj.x', 'plotrho.x', + 'pmw.x', 'pp.x', 'projwfc.x', 'pw2bgw.x', 'pw2gw.x', 'pw2wannier90.x', + 'pwcond.x', 'pw_export.x', 'pwi2xsf.x', 'pw.x', 'q2qstar.x', 'q2r.x', + 'q2trans_fd.x', 'q2trans.x', 'spectra_manipulation.x', 'sumpdos.x', + 'turbo_davidson.x', 'turbo_eels.x', 'turbo_lanczos.x', 'turbo_spectrum.x', + 'wannier_ham.x', 'wannier_plot.x', 'wfck2r.x', 'wfdd.x', 'xspectra.x']], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From dac87e7edf7d9008f3446ec222660d8d80a6963d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 9 May 2016 15:33:42 +0200 Subject: [PATCH 049/701] gensim with foss2016a --- .../gensim-0.12.4-foss-2016a-Python-2.7.11.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..4c0e09b879 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'gensim' +version = '0.12.4' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'lib' -- GitLab From f97d2048941547a82f3bad4098882834786b172c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 12:15:41 +0800 Subject: [PATCH 050/701] using updated easyblock --- ...tumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb | 81 ++++++++++++------- .../QuantumESPRESSO-5.3.0_yambo-fixes.patch | 49 +++++++++++ 2 files changed, 101 insertions(+), 29 deletions(-) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb index 91045a89e8..a8b352aa0f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -1,42 +1,65 @@ -easyblock = 'ConfigureMake' - name = 'QuantumESPRESSO' version = '5.3.0' -homepage = 'http://www.quantum-espresso.org' -description = """Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the nanoscale. - It is based on density-functional theory, plane waves, and pseudopotentials.""" +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} -source_urls = ['http://qe-forge.org/gf/download/frsrelease/204/912/'] -sources = ['espresso-%(version)s.tar.gz'] -checksums = ['6848fcfaeb118587d6be36bd10b7f2c3'] +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.tar.gz', + # must be downloaded manually from + # http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=%2F%2Acheckout%2A%2Ftags%2FQE-5.2.1%2Fespresso%2Farchive%2Fplumed-1.3-qe.tar.gz&revision=11758 + # gets updated without changes to filename, cfr. http://qe-forge.org/pipermail/q-e-commits/2015-June/007359.html + # 'plumed-1.3-qe-r11758.tar.gz', + 'pwcond-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + 'want-2.5.1-base.tar.gz', + 'yambo-3.4.1-rev61.tgz', + 'xspectra-%(version)s.tar.gz', +] +missing_sources = [ + 'sax-2.0.3.tar.gz', # nowhere to be found +] +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/204/912/', # espresso-5.3.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/184/723/', # yambo-3.4.1-rev61.tgz +] -configopts = 'DFLAGS="-D__INTEL -D__MPI -D__PARA -D__DFTI -D__SCALAPACK" ' -configopts += 'FFT_LIBS="$LIBFFT" --with-scalapack=intel ' -configopts += '--prefix=%(installdir)s/bin' +patches = [ + 'QuantumESPRESSO-%(version)s_yambo-fixes.patch', +] -buildopts = 'all' +# source checksums +checksums = [ + '6848fcfaeb118587d6be36bd10b7f2c3', # espresso-5.3.0.tar.gz + 'a1e9611b9a82941c23426028d112186e', # wannier90-1.2.tar.gz + 'e713f74b78a04600265e697ca346bea1', # atomic-5.3.0.tar.gz + '91157da66570deb4e7a353a23621a39f', # neb-5.3.0.tar.gz + '994c89e72b5500bceb44dada7134cc12', # PHonon-5.3.0.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + '897753893dc46502de24b81929694ee1', # pwcond-5.3.0.tar.gz + 'ac9d86386f2b2d28a6b00c902668669b', # tddfpt-5.3.0.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + '03ea2fda7a2f34f7d8ee6130fca23817', # yambo-3.4.1-rev61.tgz + 'fc7d9d80e00185afcab44307d3b70a65', # xspectra-5.3.0.tar.gz +] -parallel = 1 +# gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso +buildopts = 'all w90 want yambo xspectra' # plumed -sanity_check_paths = { - 'files': ['bin/' + prog for prog in ['average.x', 'bands.x', 'bgw2pw.x', 'cppp.x', - 'cp.x', 'd3.x', 'dist.x', 'dos.x', 'dynmat.x', 'epsilon.x', 'ev.x', 'fd_ef.x', - 'fd_ifc.x', 'fd.x', 'fqha.x', 'fs.x', 'generate_rVV10_kernel_table.x', - 'generate_vdW_kernel_table.x', 'importexport_binary.x', 'initial_state.x', - 'iotk_print_kinds.x', 'iotk.x', 'kpoints.x', 'lambda.x', 'ld1.x', - 'manypw.x', 'matdyn.x', 'molecularpdos.x', 'neb.x', 'path_interpolation.x', - 'phcg.x', 'ph.x', 'plan_avg.x', 'plotband.x', 'plotproj.x', 'plotrho.x', - 'pmw.x', 'pp.x', 'projwfc.x', 'pw2bgw.x', 'pw2gw.x', 'pw2wannier90.x', - 'pwcond.x', 'pw_export.x', 'pwi2xsf.x', 'pw.x', 'q2qstar.x', 'q2r.x', - 'q2trans_fd.x', 'q2trans.x', 'spectra_manipulation.x', 'sumpdos.x', - 'turbo_davidson.x', 'turbo_eels.x', 'turbo_lanczos.x', 'turbo_spectrum.x', - 'wannier_ham.x', 'wannier_plot.x', 'wfck2r.x', 'wfdd.x', 'xspectra.x']], - 'dirs': [], -} +# parallel build tends to fail +parallel = 1 moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch new file mode 100644 index 0000000000..da11a59d73 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch @@ -0,0 +1,49 @@ +* make sure -nofor_main is also used when $FC is defined as mpif90 for yambo +* fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output +--- yambo-3.4.1-rev61/configure.orig 2015-02-04 17:54:55.000000000 +0100 ++++ yambo-3.4.1-rev61/configure 2015-10-21 17:01:45.655105316 +0200 +@@ -6077,7 +6077,7 @@ + UFFLAGS="-O0 -mtune=native" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* ) +@@ -6116,7 +6116,7 @@ + UFFLAGS="-O0 -fno-second-underscore" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6159,7 +6159,7 @@ + SYSFLAGS="-O3 -w" + UFFLAGS="-O0 -w" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6212,7 +6212,7 @@ + SYSFLAGS="-O3 -w -tpp2" + UFFLAGS="-O0 -w -tpp2" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* ) +@@ -7316,7 +7316,7 @@ + + if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then + eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} +- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 ++ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 + if test -s conftest.er2 ; then + if ! test -n "`grep successful conftest.er2`" ; then + acx_F90_ok=no ; -- GitLab From f5c549eb5ae373a5dc0a957c31cada899a2f7a05 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 16 May 2016 17:00:40 +0800 Subject: [PATCH 051/701] add 5.4.0 files --- ...tumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb | 66 +++++++++++++++++++ .../QuantumESPRESSO-5.4.0_yambo-fixes.patch | 49 ++++++++++++++ 2 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000..08ae4e6988 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,66 @@ +name = 'QuantumESPRESSO' +version = '5.4.0' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.tar.gz', + # must be downloaded manually from + # http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=%2F%2Acheckout%2A%2Ftags%2FQE-5.2.1%2Fespresso%2Farchive%2Fplumed-1.3-qe.tar.gz&revision=11758 + # gets updated without changes to filename, cfr. http://qe-forge.org/pipermail/q-e-commits/2015-June/007359.html + #'plumed-1.3-qe-r11758.tar.gz', + 'pwcond-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + 'want-2.5.1-base.tar.gz', + 'yambo-3.4.1-rev61.tgz', + 'xspectra-%(version)s.tar.gz', +] +missing_sources = [ + 'sax-2.0.3.tar.gz', # nowhere to be found +] +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/184/723/', # yambo-3.4.1-rev61.tgz +] + +patches = [ + 'QuantumESPRESSO-%(version)s_yambo-fixes.patch', +] + +# source checksums +checksums = [ + '8bb78181b39bd084ae5cb7a512c1cfe7', # espresso-5.4.0.tar.gz + 'a1e9611b9a82941c23426028d112186e', # wannier90-1.2.tar.gz + '24dc0d8bf5cf4eb4dc38e1c18a80b3ee', # atomic-5.4.0.tar.gz + '254f929259fb06036b78c493cf18e5d6', # neb-5.4.0.tar.gz + 'f641fe9dcf0ec8f1e47d74e3c7c39705', # PHonon-5.4.0.tar.gz + #'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + '31c1cd8cd76752833a9205d456093d0a', # pwcond-5.4.0.tar.gz + '2101533a627644ef467b60d400977eab', # tddfpt-5.4.0.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + '03ea2fda7a2f34f7d8ee6130fca23817', # yambo-3.4.1-rev61.tgz + '95080929c87389cd15cf765048cfc9d2', # xspectra-5.4.0.tar.gz +] + +# gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso +# plumed excluded due to not finding the source package +buildopts = 'all w90 want yambo xspectra' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch new file mode 100644 index 0000000000..da11a59d73 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch @@ -0,0 +1,49 @@ +* make sure -nofor_main is also used when $FC is defined as mpif90 for yambo +* fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output +--- yambo-3.4.1-rev61/configure.orig 2015-02-04 17:54:55.000000000 +0100 ++++ yambo-3.4.1-rev61/configure 2015-10-21 17:01:45.655105316 +0200 +@@ -6077,7 +6077,7 @@ + UFFLAGS="-O0 -mtune=native" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* ) +@@ -6116,7 +6116,7 @@ + UFFLAGS="-O0 -fno-second-underscore" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6159,7 +6159,7 @@ + SYSFLAGS="-O3 -w" + UFFLAGS="-O0 -w" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6212,7 +6212,7 @@ + SYSFLAGS="-O3 -w -tpp2" + UFFLAGS="-O0 -w -tpp2" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* ) +@@ -7316,7 +7316,7 @@ + + if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then + eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} +- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 ++ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 + if test -s conftest.er2 ; then + if ! test -n "`grep successful conftest.er2`" ; then + acx_F90_ok=no ; -- GitLab From 662760e1f21edfe0f85eed40012d1be3413580b2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 18 May 2016 16:18:09 +1200 Subject: [PATCH 052/701] New generic EasyConfig for Molpro-mpp-2015.1.3 --- ...Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb new file mode 100644 index 0000000000..119e4e7dfb --- /dev/null +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb @@ -0,0 +1,21 @@ +name = 'Molpro' +versionprefix = 'mpp-' +version = '2015.1.3' +versionsuffix = '.linux_x86_64_openmp' + +homepage = 'https://www.molpro.net' +description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# no source URL available, requires registration to download +sources = ['%(namelower)s-%(versionprefix)s%(version)s%(versionsuffix)s.sh'] + +precompiled_binaries = True + +# license file - uncomment if a licence file is supplied by your site and +# is valid for all users - the value of license_file may have to be changed +#import os +#license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') + +moduleclass = 'chem' -- GitLab From a664d8bbd67211b91e95e4164f7498d17ba4cdc6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 26 May 2016 17:20:26 +0800 Subject: [PATCH 053/701] use yambo 3.4.2 --- ...tumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb | 6 +-- .../QuantumESPRESSO-5.3.0_yambo-fixes.patch | 44 ++++++++++++------- ...tumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb | 6 +-- .../QuantumESPRESSO-5.4.0_yambo-fixes.patch | 44 ++++++++++++------- 4 files changed, 60 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb index a8b352aa0f..7c819480c1 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -24,7 +24,7 @@ sources = [ 'pwcond-%(version)s.tar.gz', 'tddfpt-%(version)s.tar.gz', 'want-2.5.1-base.tar.gz', - 'yambo-3.4.1-rev61.tgz', + 'yambo-3.4.2.tgz', 'xspectra-%(version)s.tar.gz', ] missing_sources = [ @@ -34,7 +34,7 @@ source_urls = [ 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://qe-forge.org/gf/download/frsrelease/204/912/', # espresso-5.3.0.tar.gz 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz - 'http://qe-forge.org/gf/download/frsrelease/184/723/', # yambo-3.4.1-rev61.tgz + 'http://qe-forge.org/gf/download/frsrelease/208/932/', # yambo-3.4.2.tgz ] patches = [ @@ -52,7 +52,7 @@ checksums = [ '897753893dc46502de24b81929694ee1', # pwcond-5.3.0.tar.gz 'ac9d86386f2b2d28a6b00c902668669b', # tddfpt-5.3.0.tar.gz 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz - '03ea2fda7a2f34f7d8ee6130fca23817', # yambo-3.4.1-rev61.tgz + 'f0820a0f42dfc81ce3811af647bed777', # yambo-3.4.2.tgz 'fc7d9d80e00185afcab44307d3b70a65', # xspectra-5.3.0.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch index da11a59d73..6d10861729 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch @@ -1,18 +1,28 @@ * make sure -nofor_main is also used when $FC is defined as mpif90 for yambo * fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output ---- yambo-3.4.1-rev61/configure.orig 2015-02-04 17:54:55.000000000 +0100 -+++ yambo-3.4.1-rev61/configure 2015-10-21 17:01:45.655105316 +0200 -@@ -6077,7 +6077,7 @@ - UFFLAGS="-O0 -mtune=native" +author: Kenneth Hoste (HPC-UGent), adapted to espresso-5.3.0 and yambo-3.4.2 by Miguel Dias Costa (National University of Singapore) +--- espresso-5.3.0/yambo-3.4.2/configure.orig 2016-05-26 16:18:16.177156000 +0800 ++++ espresso-5.3.0/yambo-3.4.2/configure 2016-05-26 16:20:31.929218336 +0800 +@@ -6238,7 +6238,7 @@ + ;; + *g95*) + ;; +- *ifort*) ++ *ifort*|*mpif90*) + $FC -v >& ver_ + VER_8=`grep 8. ver_ | wc -l` + VER_9=`grep 9. ver_ | wc -l` +@@ -6321,7 +6321,7 @@ FCMFLAG="" + OMPFLAGS="-fopenmp" ;; - *ifort*) + *ifort*|*mpif90*) CPU_FLAG="" case "${FCVERSION}" in - *11* | *12* | *13* ) -@@ -6116,7 +6116,7 @@ - UFFLAGS="-O0 -fno-second-underscore" + *11* | *12* | *13* |*14* | *15* ) +@@ -6365,7 +6365,7 @@ + UFFLAGS="-g -O0 -fno-second-underscore" FCMFLAG="" ;; - *ifort*) @@ -20,30 +30,30 @@ CPU_FLAG="" case "${FCVERSION}" in *1*) -@@ -6159,7 +6159,7 @@ - SYSFLAGS="-O3 -w" - UFFLAGS="-O0 -w" +@@ -6413,7 +6413,7 @@ + UFFLAGS="-g -O0 -w" + OMPFLAGS="-openmp" ;; - *ifort*) + *ifort*|*mpif90*) CPU_FLAG="" case "${FCVERSION}" in *1*) -@@ -6212,7 +6212,7 @@ - SYSFLAGS="-O3 -w -tpp2" - UFFLAGS="-O0 -w -tpp2" +@@ -6472,7 +6472,7 @@ + UFFLAGS="-g -O0 -w -tpp2" + OMPFLAGS="-openmp" ;; - *ifort*) + *ifort*|*mpif90*) CPU_FLAG="" case "${FCVERSION}" in - *11* | *12* | *13* ) -@@ -7316,7 +7316,7 @@ + *11* | *12* | *13* |*14* |*15* ) +@@ -7651,7 +7651,7 @@ if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} -- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 -+ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 +- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 >&5 ++ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 >&5 if test -s conftest.er2 ; then if ! test -n "`grep successful conftest.er2`" ; then acx_F90_ok=no ; diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb index 08ae4e6988..a3d02d9d08 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb @@ -24,7 +24,7 @@ sources = [ 'pwcond-%(version)s.tar.gz', 'tddfpt-%(version)s.tar.gz', 'want-2.5.1-base.tar.gz', - 'yambo-3.4.1-rev61.tgz', + 'yambo-3.4.2.tgz', 'xspectra-%(version)s.tar.gz', ] missing_sources = [ @@ -34,7 +34,7 @@ source_urls = [ 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz - 'http://qe-forge.org/gf/download/frsrelease/184/723/', # yambo-3.4.1-rev61.tgz + 'http://qe-forge.org/gf/download/frsrelease/208/932/', # yambo-3.4.2.tgz ] patches = [ @@ -52,7 +52,7 @@ checksums = [ '31c1cd8cd76752833a9205d456093d0a', # pwcond-5.4.0.tar.gz '2101533a627644ef467b60d400977eab', # tddfpt-5.4.0.tar.gz 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz - '03ea2fda7a2f34f7d8ee6130fca23817', # yambo-3.4.1-rev61.tgz + 'f0820a0f42dfc81ce3811af647bed777', # yambo-3.4.2.tgz '95080929c87389cd15cf765048cfc9d2', # xspectra-5.4.0.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch index da11a59d73..6a1d76933b 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch @@ -1,18 +1,28 @@ * make sure -nofor_main is also used when $FC is defined as mpif90 for yambo * fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output ---- yambo-3.4.1-rev61/configure.orig 2015-02-04 17:54:55.000000000 +0100 -+++ yambo-3.4.1-rev61/configure 2015-10-21 17:01:45.655105316 +0200 -@@ -6077,7 +6077,7 @@ - UFFLAGS="-O0 -mtune=native" +author: Kenneth Hoste (HPC-UGent), adapted to espresso-5.4.0 and yambo-3.4.2 by Miguel Dias Costa (National University of Singapore) +--- espresso-5.4.0/yambo-3.4.2/configure.orig 2016-05-26 16:18:16.177156000 +0800 ++++ espresso-5.4.0/yambo-3.4.2/configure 2016-05-26 16:20:31.929218336 +0800 +@@ -6238,7 +6238,7 @@ + ;; + *g95*) + ;; +- *ifort*) ++ *ifort*|*mpif90*) + $FC -v >& ver_ + VER_8=`grep 8. ver_ | wc -l` + VER_9=`grep 9. ver_ | wc -l` +@@ -6321,7 +6321,7 @@ FCMFLAG="" + OMPFLAGS="-fopenmp" ;; - *ifort*) + *ifort*|*mpif90*) CPU_FLAG="" case "${FCVERSION}" in - *11* | *12* | *13* ) -@@ -6116,7 +6116,7 @@ - UFFLAGS="-O0 -fno-second-underscore" + *11* | *12* | *13* |*14* | *15* ) +@@ -6365,7 +6365,7 @@ + UFFLAGS="-g -O0 -fno-second-underscore" FCMFLAG="" ;; - *ifort*) @@ -20,30 +30,30 @@ CPU_FLAG="" case "${FCVERSION}" in *1*) -@@ -6159,7 +6159,7 @@ - SYSFLAGS="-O3 -w" - UFFLAGS="-O0 -w" +@@ -6413,7 +6413,7 @@ + UFFLAGS="-g -O0 -w" + OMPFLAGS="-openmp" ;; - *ifort*) + *ifort*|*mpif90*) CPU_FLAG="" case "${FCVERSION}" in *1*) -@@ -6212,7 +6212,7 @@ - SYSFLAGS="-O3 -w -tpp2" - UFFLAGS="-O0 -w -tpp2" +@@ -6472,7 +6472,7 @@ + UFFLAGS="-g -O0 -w -tpp2" + OMPFLAGS="-openmp" ;; - *ifort*) + *ifort*|*mpif90*) CPU_FLAG="" case "${FCVERSION}" in - *11* | *12* | *13* ) -@@ -7316,7 +7316,7 @@ + *11* | *12* | *13* |*14* |*15* ) +@@ -7651,7 +7651,7 @@ if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} -- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 -+ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 +- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 >&5 ++ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 >&5 if test -s conftest.er2 ; then if ! test -n "`grep successful conftest.er2`" ; then acx_F90_ok=no ; -- GitLab From 6fe9a26f678b2d4ab0f124abefdca37f9a93a6e3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 26 May 2016 17:21:47 +0800 Subject: [PATCH 054/701] apply FFTXlib patch --- ...tumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb | 1 + .../QuantumESPRESSO-5.3.0_fftxlib-fixes.patch | 24 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_fftxlib-fixes.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb index 7c819480c1..47409915bd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -39,6 +39,7 @@ source_urls = [ patches = [ 'QuantumESPRESSO-%(version)s_yambo-fixes.patch', + 'QuantumESPRESSO-%(version)s_fftxlib-fixes.patch', ] # source checksums diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_fftxlib-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_fftxlib-fixes.patch new file mode 100644 index 0000000000..c1fdcc9873 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_fftxlib-fixes.patch @@ -0,0 +1,24 @@ +* remove fftw_version, conflicts with the one in mkl's fftw +* http://qe-forge.org/pipermail/q-e-developers/2016-January/001088.html +author: Miguel Dias Costa (National University of Singapore) +--- espresso-5.3.0/FFTXlib/fftw.c.orig 2016-05-26 09:54:35.911733000 +0800 ++++ espresso-5.3.0/FFTXlib/fftw.c 2016-05-26 09:59:43.900568303 +0800 +@@ -345,8 +345,6 @@ + #include + #include + +-char *fftw_version = "FFTW V1.1 ($Id: fftw.c,v 1.3 2010-01-26 14:06:59 giannozz Exp $)"; +- + /* + * This function is called in other files, so we cannot declare + * it as static. +--- espresso-5.3.0/FFTXlib/fftw.h.orig 2016-05-26 09:54:40.566922000 +0800 ++++ espresso-5.3.0/FFTXlib/fftw.h 2016-05-26 09:59:59.822132168 +0800 +@@ -133,7 +133,6 @@ + + extern generic_codelet fftw_twiddle_generic; + extern generic_codelet fftwi_twiddle_generic; +-extern char *fftw_version; + + /***************************** + * Plans -- GitLab From 824522c01ae2bd1ba8c36c810e6294fd2ea546ba Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 26 May 2016 17:23:27 +0800 Subject: [PATCH 055/701] workaround for missing upftools in espresso-5.3.0 --- .../QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb index 47409915bd..7bd4242d31 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -58,7 +58,9 @@ checksums = [ ] # gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso -buildopts = 'all w90 want yambo xspectra' # plumed +# add plumed and uncomment the lines in sources and checksums if the package is downloaded manually +# 'all' not used here because upftools are missing from 5.3.0 package +buildopts = 'pw ph pp pwcond neb cp ld1 tddfpt w90 want yambo xspectra' # plumed # parallel build tends to fail parallel = 1 -- GitLab From c9975a0e9c35a8d68d2aa91c2e882dccebf84d08 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 26 May 2016 17:24:03 +0800 Subject: [PATCH 056/701] fix style --- .../QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb index a3d02d9d08..8529a9282f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb @@ -20,7 +20,7 @@ sources = [ # must be downloaded manually from # http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=%2F%2Acheckout%2A%2Ftags%2FQE-5.2.1%2Fespresso%2Farchive%2Fplumed-1.3-qe.tar.gz&revision=11758 # gets updated without changes to filename, cfr. http://qe-forge.org/pipermail/q-e-commits/2015-June/007359.html - #'plumed-1.3-qe-r11758.tar.gz', + # 'plumed-1.3-qe-r11758.tar.gz', 'pwcond-%(version)s.tar.gz', 'tddfpt-%(version)s.tar.gz', 'want-2.5.1-base.tar.gz', @@ -48,7 +48,7 @@ checksums = [ '24dc0d8bf5cf4eb4dc38e1c18a80b3ee', # atomic-5.4.0.tar.gz '254f929259fb06036b78c493cf18e5d6', # neb-5.4.0.tar.gz 'f641fe9dcf0ec8f1e47d74e3c7c39705', # PHonon-5.4.0.tar.gz - #'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz '31c1cd8cd76752833a9205d456093d0a', # pwcond-5.4.0.tar.gz '2101533a627644ef467b60d400977eab', # tddfpt-5.4.0.tar.gz 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz @@ -57,8 +57,8 @@ checksums = [ ] # gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso -# plumed excluded due to not finding the source package -buildopts = 'all w90 want yambo xspectra' +# add plumed and uncomment the lines in sources and checksums if the package is downloaded manually +buildopts = 'all w90 want yambo xspectra' # plumed # parallel build tends to fail parallel = 1 -- GitLab From 9f0ca23989dc0bc89ca8a406910598796790a43d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 27 May 2016 14:21:57 +0800 Subject: [PATCH 057/701] temporarily disable yambo --- .../QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb | 3 ++- .../QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb index 7bd4242d31..27aa697f25 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -58,9 +58,10 @@ checksums = [ ] # gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso +# yambo excluded due to netcdf errors # add plumed and uncomment the lines in sources and checksums if the package is downloaded manually # 'all' not used here because upftools are missing from 5.3.0 package -buildopts = 'pw ph pp pwcond neb cp ld1 tddfpt w90 want yambo xspectra' # plumed +buildopts = 'pw ph pp pwcond neb cp ld1 tddfpt w90 want xspectra' # yambo plumed # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb index 8529a9282f..a1b3097cea 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb @@ -57,8 +57,9 @@ checksums = [ ] # gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso +# yambo excluded due to netcdf errors # add plumed and uncomment the lines in sources and checksums if the package is downloaded manually -buildopts = 'all w90 want yambo xspectra' # plumed +buildopts = 'all w90 want xspectra' # yambo plumed # parallel build tends to fail parallel = 1 -- GitLab From cb5fcdf1c7e99157dd470decc26847f083db3967 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 2 Jun 2016 09:49:53 +0200 Subject: [PATCH 058/701] Remove unused easyconfigs --- .../l/libxc/libxc-2.2.2-intel-2016a.eb | 32 -------------- .../p/PLUMED/PLUMED-2.2.1-intel-2016a.eb | 42 ------------------- 2 files changed, 74 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb deleted file mode 100644 index 959f0d1356..0000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2016a.eb +++ /dev/null @@ -1,32 +0,0 @@ -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': '2016a'} -toolchainopts = {'opt': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] - -configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' - -# From the libxc mailing list -# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -# a fully working testsuite soon (unless someone wants to volunteer to do -# it, of course ) In the meantime, unless the majority of the tests -# fail, your build should be fine. -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb deleted file mode 100644 index eff628072a..0000000000 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.1-intel-2016a.eb +++ /dev/null @@ -1,42 +0,0 @@ -# by Ward Poelmans - -easyblock = 'ConfigureMake' - -name = 'PLUMED' -version = '2.2.1' - -homepage = 'http://www.plumed-code.org' -description = """PLUMED is an open source library for free energy calculations in molecular systems which - works together with some of the most popular molecular dynamics engines. Free energy calculations can be - performed as a function of many order parameters with a particular focus on biological problems, using - state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. - The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. -""" - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'usempi': 'True'} - -source_urls = ['https://github.com/plumed/plumed2/archive/'] -sources = ['v%(version)s.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), - ('GSL', '2.1'), - ('libmatheval', '1.1.11'), -] - -preconfigopts = 'FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' -configopts = ' --exec-prefix=%(installdir)s --enable-gsl' -prebuildopts = 'source sourceme.sh && ' - -sanity_check_paths = { - 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], - 'dirs': ['lib/plumed'] -} - -modextrapaths = { - 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, - 'PLUMED_ROOT': 'lib/plumed', -} - -moduleclass = 'chem' -- GitLab From 04ecfa6a89d8955a1e590ba902ae8f95ef98ea38 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 2 Jun 2016 19:34:56 +0800 Subject: [PATCH 059/701] re-enable yambo --- .../QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb | 3 +-- .../QuantumESPRESSO-5.3.0_yambo-fixes.patch | 12 ++++++++++++ .../QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb | 3 +-- .../QuantumESPRESSO-5.4.0_yambo-fixes.patch | 12 ++++++++++++ 4 files changed, 26 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb index 27aa697f25..7bd4242d31 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -58,10 +58,9 @@ checksums = [ ] # gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso -# yambo excluded due to netcdf errors # add plumed and uncomment the lines in sources and checksums if the package is downloaded manually # 'all' not used here because upftools are missing from 5.3.0 package -buildopts = 'pw ph pp pwcond neb cp ld1 tddfpt w90 want xspectra' # yambo plumed +buildopts = 'pw ph pp pwcond neb cp ld1 tddfpt w90 want yambo xspectra' # plumed # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch index 6d10861729..b4c96acc60 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch @@ -1,5 +1,6 @@ * make sure -nofor_main is also used when $FC is defined as mpif90 for yambo * fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output +* force ifort mangling in yambo's netcdf author: Kenneth Hoste (HPC-UGent), adapted to espresso-5.3.0 and yambo-3.4.2 by Miguel Dias Costa (National University of Singapore) --- espresso-5.3.0/yambo-3.4.2/configure.orig 2016-05-26 16:18:16.177156000 +0800 +++ espresso-5.3.0/yambo-3.4.2/configure 2016-05-26 16:20:31.929218336 +0800 @@ -57,3 +58,14 @@ author: Kenneth Hoste (HPC-UGent), adapted to espresso-5.3.0 and yambo-3.4.2 by if test -s conftest.er2 ; then if ! test -n "`grep successful conftest.er2`" ; then acx_F90_ok=no ; +--- espresso-5.3.0/yambo-3.4.2/lib/netcdf/Makefile.loc.orig 2016-06-02 17:29:53.816844000 +0800 ++++ espresso-5.3.0/yambo-3.4.2/lib/netcdf/Makefile.loc 2016-06-02 17:30:45.579476000 +0800 +@@ -40,7 +40,7 @@ + FC="$(f90)" \ + FCFLAGS="$(f77flags)" \ + FFLAGS="$(f77flags)" \ +- CPPFLAGS="$(netcdf_aux)" \ ++ CPPFLAGS="$(netcdf_aux) -DpgiFortran" \ + F90="$(f90)" \ + F77="$(f77)" \ + INSTALL_DIR="$(INSTALL_DIR)" ); \ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb index a1b3097cea..8529a9282f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb @@ -57,9 +57,8 @@ checksums = [ ] # gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso -# yambo excluded due to netcdf errors # add plumed and uncomment the lines in sources and checksums if the package is downloaded manually -buildopts = 'all w90 want xspectra' # yambo plumed +buildopts = 'all w90 want yambo xspectra' # plumed # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch index 6a1d76933b..fd63a36333 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch @@ -1,5 +1,6 @@ * make sure -nofor_main is also used when $FC is defined as mpif90 for yambo * fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output +* force ifort mangling in yambo's netcdf author: Kenneth Hoste (HPC-UGent), adapted to espresso-5.4.0 and yambo-3.4.2 by Miguel Dias Costa (National University of Singapore) --- espresso-5.4.0/yambo-3.4.2/configure.orig 2016-05-26 16:18:16.177156000 +0800 +++ espresso-5.4.0/yambo-3.4.2/configure 2016-05-26 16:20:31.929218336 +0800 @@ -57,3 +58,14 @@ author: Kenneth Hoste (HPC-UGent), adapted to espresso-5.4.0 and yambo-3.4.2 by if test -s conftest.er2 ; then if ! test -n "`grep successful conftest.er2`" ; then acx_F90_ok=no ; +--- espresso-5.4.0/yambo-3.4.2/lib/netcdf/Makefile.loc.orig 2016-06-02 17:29:53.816844000 +0800 ++++ espresso-5.4.0/yambo-3.4.2/lib/netcdf/Makefile.loc 2016-06-02 17:30:45.579476000 +0800 +@@ -40,7 +40,7 @@ + FC="$(f90)" \ + FCFLAGS="$(f77flags)" \ + FFLAGS="$(f77flags)" \ +- CPPFLAGS="$(netcdf_aux)" \ ++ CPPFLAGS="$(netcdf_aux) -DpgiFortran" \ + F90="$(f90)" \ + F77="$(f77)" \ + INSTALL_DIR="$(INSTALL_DIR)" ); \ -- GitLab From fb5150e9d1dcc67c922cfa1c5de748b0d1ccef5f Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Sat, 4 Jun 2016 15:30:00 +0200 Subject: [PATCH 060/701] modify easyconfig ParaView-4.4.0-intel-2016a.eb, add easyconfig ParaView-4.4.0-foss-2016a.eb --- .../p/ParaView/ParaView-4.4.0-foss-2016a.eb | 47 +++++++++++++++++++ .../p/ParaView/ParaView-4.4.0-intel-2016a.eb | 2 + 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-foss-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-foss-2016a.eb new file mode 100644 index 0000000000..ffa008562b --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-foss-2016a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '4.4.0' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': False} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s-source.tar.gz"] + +patches = ['%(name)s-%(version)s_missingheader.patch'] + +dependencies = [ + ('libGLU', '9.0.0', '-Mesa-11.2.1'), + ('libXt', '1.1.5'), + ('Qt', '4.8.7'), + ('libXext', '1.3.3'), + ('libX11', '1.6.3'), + ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial'), +] + +builddependencies = [('CMake', '3.5.2')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb index 838808a743..0197db6977 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libX11', '1.6.3'), ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial'), ] builddependencies = [('CMake', '3.5.2')] @@ -31,6 +32,7 @@ separate_build_dir = True configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # Without internet connection turn off testing (uncomment the following line) configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md -- GitLab From 3543f15ff900558ef4fd59e6de496d737578e2ec Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Sun, 5 Jun 2016 22:47:51 +0200 Subject: [PATCH 061/701] Apply changes to other ParaView 4.4.0 and add required dependencies --- .../h/HDF5/HDF5-1.8.16-GCC-4.9.3-serial.eb | 22 ++++++++++++++++++ .../ParaView-4.4.0-gimkl-2.11.5-mpi.eb | 2 ++ .../ParaView-4.4.0-intel-2015b-mpi.eb | 2 ++ .../p/ParaView/ParaView-4.4.0-intel-2015b.eb | 2 ++ .../easyconfigs/s/Szip/Szip-2.1-GCC-4.9.3.eb | 23 +++++++++++++++++++ 5 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-GCC-4.9.3-serial.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-GCC-4.9.3.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-GCC-4.9.3-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-GCC-4.9.3-serial.eb new file mode 100644 index 0000000000..520a546466 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-GCC-4.9.3-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.16' +versionsuffix = '-serial' + +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': 'GCC', 'version': '4.9.3'} +toolchainopts = {'optarch': True, 'pic': 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/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb index a0d908d3d5..366ab8e374 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb @@ -27,6 +27,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libX11', '1.6.3'), ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial', ('GCC', '4.9.3')), ] builddependencies = [('CMake', '3.4.3')] @@ -38,6 +39,7 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # Without internet connection turn off testing (uncomment the following line) #configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb index 2e7bc45270..c47c9437bd 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb @@ -27,6 +27,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libX11', '1.6.3', pysuff), ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial'), ] builddependencies = [('CMake', '3.3.2')] @@ -38,6 +39,7 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # Without internet connection turn off testing (uncomment the following line) #configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb index 0057213bea..bd0d7b5f22 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb @@ -26,6 +26,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libX11', '1.6.3', pysuff), ('zlib', '1.2.8'), + ('HDF5', '1.8.16', '-serial'), ] builddependencies = [('CMake', '3.3.2')] @@ -37,6 +38,7 @@ maxparallel = 4 configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON ' configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # Without internet connection turn off testing (uncomment the following line) #configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-GCC-4.9.3.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-GCC-4.9.3.eb new file mode 100644 index 0000000000..06743759f2 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-GCC-4.9.3.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': 'GCC', 'version': '4.9.3'} +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.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 26ec235e0fc1908754b3e68bb962040d2aea0742 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Mon, 6 Jun 2016 15:32:57 +0200 Subject: [PATCH 062/701] Use dependencies based on gimkl/2.11.5 for ParaView 4.4.0 with gimkl/2.11.5 --- ...6-GCC-4.9.3-serial.eb => HDF5-1.8.16-gimkl-2.11.5-serial.eb} | 2 +- .../easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb | 2 +- .../s/Szip/{Szip-2.1-GCC-4.9.3.eb => Szip-2.1-gimkl-2.11.5.eb} | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.8.16-GCC-4.9.3-serial.eb => HDF5-1.8.16-gimkl-2.11.5-serial.eb} (91%) rename easybuild/easyconfigs/s/Szip/{Szip-2.1-GCC-4.9.3.eb => Szip-2.1-gimkl-2.11.5.eb} (92%) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-GCC-4.9.3-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb similarity index 91% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-GCC-4.9.3-serial.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb index 520a546466..2130c99fd6 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-GCC-4.9.3-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb @@ -6,7 +6,7 @@ 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': 'GCC', 'version': '4.9.3'} +toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb index 366ab8e374..358fff80d8 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb @@ -27,7 +27,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libX11', '1.6.3'), ('zlib', '1.2.8'), - ('HDF5', '1.8.16', '-serial', ('GCC', '4.9.3')), + ('HDF5', '1.8.16', '-serial'), ] builddependencies = [('CMake', '3.4.3')] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-GCC-4.9.3.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.eb similarity index 92% rename from easybuild/easyconfigs/s/Szip/Szip-2.1-GCC-4.9.3.eb rename to easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.eb index 06743759f2..37afd28477 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.eb @@ -6,7 +6,7 @@ version = '2.1' homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" -toolchain = {'name': 'GCC', 'version': '4.9.3'} +toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -- GitLab From c0d2f6e911726f84afa893596725232a69fe9e10 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 4 Jul 2016 10:52:14 +0200 Subject: [PATCH 063/701] OpenBabel with foss2016a --- ...penBabel-2.3.2-foss-2016a-Python-2.7.11.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a511a38eb3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +name = 'OpenBabel' +version = '2.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'OpenBabel-%(version)s-fix-link-path-tests.patch', + 'OpenBabel-%(version)s-ignore-failed-test.patch', +] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +dependencies = [ + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), + ('Eigen', '3.2.8'), +] + +runtest = 'test' + +moduleclass = 'chem' -- GitLab From c186a24362bf5e33049813a424c60d9deb65c07c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 4 Jul 2016 11:38:56 +0200 Subject: [PATCH 064/701] PETSc with foss2016a --- .../PETSc-3.7.2-foss-2016a-Python-2.7.11.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.7.2-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a5fcbdc035 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +name = 'PETSc' +version = '3.7.2' +versionsuffix = '-Python-2.7.11' + +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': 'foss', 'version': '2016a'} +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', '1.61.0', versionsuffix), + ('ScientificPython', '2.9.4', versionsuffix), + ('FIAT', '1.6.0', versionsuffix), + ('METIS', '5.1.0'), + (parmetis, parmetis_ver), + ('SCOTCH', '6.0.4'), + ('SuiteSparse', '4.5.3', '-%s-%s' % (parmetis, parmetis_ver)), + ('Hypre', '2.11.1'), +] + +builddependencies = [('CMake', '3.5.2')] + +moduleclass = 'numlib' -- GitLab From ac4519c4074272c78916c7a23250ee5f2d39e862 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 4 Jul 2016 11:39:49 +0200 Subject: [PATCH 065/701] SuiteSparse-ParMETIS dep of PETSc --- ...eSparse-4.5.3-foss-2016a-ParMETIS-4.0.3.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-foss-2016a-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-foss-2016a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-foss-2016a-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000..3b604c9d6d --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-foss-2016a-ParMETIS-4.0.3.eb @@ -0,0 +1,20 @@ +name = 'SuiteSparse' +version = '4.5.3' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +versionsuffix = '-%s-%s' % (parmetis, parmetis_ver) +dependencies = [(parmetis, parmetis_ver)] + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From fdb10e11a9e386f1368aaae37d95306630956c14 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 4 Jul 2016 13:35:48 +0200 Subject: [PATCH 066/701] PLAST with foss2016a --- .../p/PLAST/PLAST-2.3.1-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb new file mode 100644 index 0000000000..f8d5b9f38b --- /dev/null +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'PLAST' +version = '2.3.1' + +homepage = "http://www.irisa.fr/symbiose/projects/plast/" +description = """ +PLAST is a parallel alignment search tool for comparing large protein banks +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/PLAST-software/plast-library/releases/download/v2.3.1/'] +sources=['%(namelower)s_source_v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'include/algo', 'include/alignment', 'include/misc'], +} + +moduleclass = 'bio' -- GitLab From 98b0be06a95eb8e1081e31662889646f4457e848 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 7 Jul 2016 13:14:01 +0200 Subject: [PATCH 067/701] style changes --- easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb index f8d5b9f38b..1baf1e7347 100644 --- a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb @@ -4,13 +4,11 @@ name = 'PLAST' version = '2.3.1' homepage = "http://www.irisa.fr/symbiose/projects/plast/" -description = """ -PLAST is a parallel alignment search tool for comparing large protein banks -""" +description = """PLAST is a parallel alignment search tool for comparing large protein banks""" toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https://github.com/PLAST-software/plast-library/releases/download/v2.3.1/'] +source_urls = ['https://github.com/PLAST-software/plast-library/releases/download/v%(version)s/'] sources=['%(namelower)s_source_v%(version)s.tar.gz'] builddependencies = [('CMake', '3.5.2')] @@ -20,4 +18,4 @@ sanity_check_paths = { 'dirs': ['include', 'include/algo', 'include/alignment', 'include/misc'], } -moduleclass = 'bio' +moduleclass = 'bio' \ No newline at end of file -- GitLab From a5acaa1048d3e746a2d527676f0361a8700d2929 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 7 Jul 2016 13:16:12 +0200 Subject: [PATCH 068/701] Eigen dep --- .../easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb new file mode 100644 index 0000000000..99e9f6bd51 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.8' + +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': '2016a'} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 22a47b2ee784e3aceb1fd07b45abb240f91c14de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Jul 2016 14:23:49 +0200 Subject: [PATCH 069/701] add easyconfig Qt5-5.7.0-intel-2016a.eb --- .../q/Qt5/Qt5-5.7.0-intel-2016a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb new file mode 100644 index 0000000000..82e71ce75d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb @@ -0,0 +1,53 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +builddependencies = [ + ('fixesproto', '5.0'), + ('glproto', '1.4.17'), + ('inputproto', '2.3.1'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('pkg-config', '0.29.1'), + ('xcb-proto', '1.11', '', True), + ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +moduleclass = 'devel' -- GitLab From 7735d88661187dba4fa0ce881c7932d1059cfe08 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 8 Jul 2016 17:56:56 +0200 Subject: [PATCH 070/701] Adjust for new easyblock --- .../easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb | 2 -- .../easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb index 9d52b0ef88..ed0569f101 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb @@ -33,8 +33,6 @@ builddependencies = [ ] configopts = '-DENABLE_MPI=ON -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_CHEMPS2=ON -DENABLE_PLUGINS=ON' -configopts += ' -DENABLE_DUMMY_PLUGIN=ON -DCHEMPS2_ROOT=$EBROOTCHEMPS2' -configopts += ' -DENABLE_PCMSOLVER=ON -DPCMSOLVER_ROOT=$EBROOTPCMSOLVER' # CMake will pick mpiexec by default and this fails with intel MPI #configopts += ' -DMPIEXEC=$EBROOTIMPI/bin64/mpirun' diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb index 90a8852122..1fcbf7998b 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb @@ -34,8 +34,6 @@ builddependencies = [ ] configopts = '-DENABLE_MPI=OFF -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_PLUGINS=ON -DENABLE_DUMMY_PLUGIN=ON' -configopts += ' -DENABLE_CHEMPS2=ON -DCHEMPS2_ROOT=$EBROOTCHEMPS2' -configopts += ' -DENABLE_PCMSOLVER=ON -DPCMSOLVER_ROOT=$EBROOTPCMSOLVER' # Execute 4 tests in parallel and disable the pubchem tests (they download things and don't work reliable) # Limit the number of concurrent tests to avoid failures -- GitLab From a9d2a807dae619bb9ecff9ab90f03badcad5e7ba Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 10 Jul 2016 16:46:15 +0200 Subject: [PATCH 071/701] psortb with foss2016a --- .../BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb | 38 ++++++++++++++++ .../PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 45 +++++++++++++++++++ .../p/pftools/pftools-V3-foss-2016a.eb | 21 +++++++++ 3 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSORTb/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb create mode 100644 easybuild/easyconfigs/p/pftools/pftools-V3-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PSORTb/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSORTb/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..c7b71288fa --- /dev/null +++ b/easybuild/easyconfigs/p/PSORTb/BLAST+-2.3.0-foss-2016a-Python-2.7.11.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 , 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 = '2.3.0' +versionsuffix = '-Python-2.7.11' + +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': '2016a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000..cf6f610714 --- /dev/null +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,45 @@ +easyblock = 'PerlModule' + +name = 'PSORTb' +version = '3.0.4' + +homepage = 'http://psort.org/psortb/index.html' +description = """PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.psort.org/download/'] +sources = ['bio-tools-psort-all.%(version)s.tar.gz'] + +patches = ['PSORTb-3.03-libpsortb.patch'] + +perl = 'Perl' +perlver = '5.22.1' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('libpsortb','1.0'), + ('BioPerl','1.6.924','-Perl-5.22.1'), + ('BLAST+','2.3.0', '-Python-2.7.11'), + ('pftools','2.3'), +] +#BLAST+ instead of BLAST? + +options = {'modulename': 'Bio::Tools::PSort'} + +preconfigopts = "export PSORTROOT=%(installdir)s && " + +postinstallcmds = [ + "cp -r psort/* %(installdir)s/.", +] + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Algorithm/HMM.pm' % (perlmajver, perlver), + 'lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Algorithm/HMM' % (perlmajver, perlver), + 'lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Bio/Tools/PSort' % (perlmajver, perlver)], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pftools/pftools-V3-foss-2016a.eb b/easybuild/easyconfigs/p/pftools/pftools-V3-foss-2016a.eb new file mode 100644 index 0000000000..e42e2a92c5 --- /dev/null +++ b/easybuild/easyconfigs/p/pftools/pftools-V3-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock='ConfigureMake' + +name = 'pftools' +version = 'V3' + +homepage = 'http://web.expasy.org/pftools/' +description = """The pftools package contains all the software necessary to build protein and DNA generalized profiles and use + them to scan and align sequences, and search databases. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = ['ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/pftoolsV3/'] + +sanity_check_paths = { + 'files': ['bin/ptof', 'bin/htop', 'bin/6ft', 'bin/2ft', 'bin/pfdump', 'bin/pfscan', 'bin/pfsearch'], + 'dirs': [], +} + +moduleclass = 'bio' \ No newline at end of file -- GitLab From f43ff29070d706118da75e039f4cf135126f770c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 10 Jul 2016 16:50:17 +0200 Subject: [PATCH 072/701] BLAST+ in BLAST+ folder --- .../PSORTb => b/BLAST+}/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb | 0 .../easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 1 - 2 files changed, 1 deletion(-) rename easybuild/easyconfigs/{p/PSORTb => b/BLAST+}/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb (100%) diff --git a/easybuild/easyconfigs/p/PSORTb/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/p/PSORTb/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index cf6f610714..8bd87b07e3 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -24,7 +24,6 @@ dependencies = [ ('BLAST+','2.3.0', '-Python-2.7.11'), ('pftools','2.3'), ] -#BLAST+ instead of BLAST? options = {'modulename': 'Bio::Tools::PSort'} -- GitLab From a0b242a5b3c1bd3059fb90b142168eef8e90ec3a Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 10 Jul 2016 18:28:18 +0200 Subject: [PATCH 073/701] include patch --- .../p/PSORTb/PSORTb-3.0.4-libpsortb.patch | 128 ++++++++++++++++++ 1 file changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch new file mode 100644 index 0000000000..77c77af3b7 --- /dev/null +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch @@ -0,0 +1,128 @@ +diff -ru bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm +--- bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm 2010-07-29 00:12:43.000000000 +0200 ++++ bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm 2015-11-26 13:50:18.000000000 +0100 +@@ -77,7 +77,12 @@ + } + } + } else { +- $input = ExtUtils::MakeMaker::prompt("\n$lib was not found in the dynamic linker path, is there somewhere else we should check? ", "/usr/local/lib$sixtyfour"); ++ if (exists($ENV{EBROOTLIBPSORTB})) { ++ $input = "$ENV{EBROOTLIBPSORTB}/lib$sixtyfour"; ++ } else { ++ $input = "/usr/local/lib$sixtyfour"; ++ } ++ $input = ExtUtils::MakeMaker::prompt("\n$lib was not found in the dynamic linker path, is there somewhere else we should check? ", $input); + if($path = Bio::Tools::PSort::Install->findLib("-L$input -l$lib")) { + $passed = 1; + $libpath = $input; +diff -ru bio-tools-psort-all/Makefile.PL bio-tools-psort-all.new/Makefile.PL +--- bio-tools-psort-all/Makefile.PL 2010-07-28 23:40:19.000000000 +0200 ++++ bio-tools-psort-all.new/Makefile.PL 2015-11-30 12:03:14.000000000 +0100 +@@ -97,7 +97,12 @@ + } + + sub get_psort_root { +- my $root = prompt("Where do you plan to install the psort configuration files?", '/usr/local/psortb'); ++ if(exists($ENV{PSORTROOT})) { ++ $root = $ENV{PSORTROOT}; ++ } else { ++ $root = '/usr/local/psortb'; ++ } ++ my $root = prompt("Where do you plan to install the psort configuration files?", $root); + $PSORT_ROOT = $root; + } + +Only in bio-tools-psort-all: .Makefile.PL.swp +diff -ru bio-tools-psort-all/psort/bin/check-sig bio-tools-psort-all.new/psort/bin/check-sig +--- bio-tools-psort-all/psort/bin/check-sig 2003-07-25 18:48:03.000000000 +0200 ++++ bio-tools-psort-all.new/psort/bin/check-sig 2015-11-26 13:51:19.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/bin/psort bio-tools-psort-all.new/psort/bin/psort +--- bio-tools-psort-all/psort/bin/psort 2010-05-26 23:51:55.000000000 +0200 ++++ bio-tools-psort-all.new/psort/bin/psort 2015-11-26 13:50:58.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Bio::Tools::PSort::Report::Formatter; + use Bio::Tools::PSort; +diff -ru bio-tools-psort-all/psort/bin/psort.tmpt bio-tools-psort-all.new/psort/bin/psort.tmpt +--- bio-tools-psort-all/psort/bin/psort.tmpt 2009-11-10 22:46:09.000000000 +0100 ++++ bio-tools-psort-all.new/psort/bin/psort.tmpt 2015-11-26 13:51:01.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Bio::Tools::PSort::Report::Formatter; + use Bio::Tools::PSort; +diff -ru bio-tools-psort-all/psort/conf/analysis/signal/archaea/check-sig bio-tools-psort-all.new/psort/conf/analysis/signal/archaea/check-sig +--- bio-tools-psort-all/psort/conf/analysis/signal/archaea/check-sig 2008-10-01 18:57:37.000000000 +0200 ++++ bio-tools-psort-all.new/psort/conf/analysis/signal/archaea/check-sig 2015-11-26 13:52:00.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/conf/analysis/signal/gramneg/check-sig bio-tools-psort-all.new/psort/conf/analysis/signal/gramneg/check-sig +--- bio-tools-psort-all/psort/conf/analysis/signal/gramneg/check-sig 2004-02-25 08:50:44.000000000 +0100 ++++ bio-tools-psort-all.new/psort/conf/analysis/signal/gramneg/check-sig 2015-11-26 13:52:02.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/conf/analysis/signal/grampos/check-sig bio-tools-psort-all.new/psort/conf/analysis/signal/grampos/check-sig +--- bio-tools-psort-all/psort/conf/analysis/signal/grampos/check-sig 2004-04-02 20:23:28.000000000 +0200 ++++ bio-tools-psort-all.new/psort/conf/analysis/signal/grampos/check-sig 2015-11-26 13:52:05.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/server/rpc/classify.xpl bio-tools-psort-all.new/psort/server/rpc/classify.xpl +--- bio-tools-psort-all/psort/server/rpc/classify.xpl 2004-03-05 20:47:06.000000000 +0100 ++++ bio-tools-psort-all.new/psort/server/rpc/classify.xpl 2015-11-26 13:52:20.000000000 +0100 +@@ -14,7 +14,7 @@ + + + Date: Sun, 10 Jul 2016 18:29:52 +0200 Subject: [PATCH 074/701] include patch --- .../easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index 8bd87b07e3..55574b78fe 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.psort.org/download/'] sources = ['bio-tools-psort-all.%(version)s.tar.gz'] -patches = ['PSORTb-3.03-libpsortb.patch'] +patches = ['PSORTb-%(version)s-libpsortb.patch'] perl = 'Perl' perlver = '5.22.1' -- GitLab From 14408cd34f9b6a011f48245e3cccf5c388b2b904 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 10 Jul 2016 18:39:00 +0200 Subject: [PATCH 075/701] PCRE2 with foss2016a --- .../p/PCRE2/PCRE2-10.21-foss-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb new file mode 100644 index 0000000000..8f16d58e42 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.21' + +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': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-jit" + +moduleclass = 'devel' -- GitLab From 73f1e6ac6ba154fdadc32b631f2d075d3bb20818 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 10 Jul 2016 20:19:49 +0200 Subject: [PATCH 076/701] add easyconfig Qt5-5.7.0-foss-2016a.eb --- .../easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb new file mode 100644 index 0000000000..50c78a140e --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb @@ -0,0 +1,53 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +builddependencies = [ + ('fixesproto', '5.0'), + ('glproto', '1.4.17'), + ('inputproto', '2.3.1'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('pkg-config', '0.29.1'), + ('xcb-proto', '1.11', '', True), + ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('GLib', '2.48.0'), + ('libX11', '1.6.3'), + ('libXt', '1.1.5'), + ('libXi', '1.7.6'), + ('xcb-util', '0.4.0'), + ('xcb-util-image', '0.4.0'), + ('xcb-util-keysyms', '0.4.0'), + ('xcb-util-renderutil', '0.3.9'), + ('xcb-util-wm', '0.4.1'), + ('libxkbcommon', '0.6.1'), + ('libXrender', '0.9.9'), + ('fontconfig', '2.11.95'), + ('freetype', '2.6.3'), + ('libXfixes', '5.0.1'), + ('libXcursor', '1.1.14'), + ('libXinerama', '1.1.3'), + ('libXrandr', '1.5.0'), + ('libpng', '1.6.21'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +moduleclass = 'devel' \ No newline at end of file -- GitLab From 27466099d66e638882fa7a7f419a3153a103d991 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 12 Jul 2016 18:42:54 +0200 Subject: [PATCH 077/701] pftools rename, perlversion used properly --- .../PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 15 ++++++--------- .../p/PSORTb/PSORTb-3.0.4-libpsortb.patch | 2 ++ ...-2016a.eb => pftoolsV3-24.03.16-foss-2016a.eb} | 9 +++++---- 3 files changed, 13 insertions(+), 13 deletions(-) rename easybuild/easyconfigs/p/pftools/{pftools-V3-foss-2016a.eb => pftoolsV3-24.03.16-foss-2016a.eb} (76%) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index 55574b78fe..b74de25012 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -2,6 +2,7 @@ easyblock = 'PerlModule' name = 'PSORTb' version = '3.0.4' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://psort.org/psortb/index.html' description = """PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.""" @@ -13,12 +14,8 @@ sources = ['bio-tools-psort-all.%(version)s.tar.gz'] patches = ['PSORTb-%(version)s-libpsortb.patch'] -perl = 'Perl' -perlver = '5.22.1' -versionsuffix = '-%s-%s' % (perl, perlver) - dependencies = [ - (perl, perlver), + ('Perl', '5.22.1'), ('libpsortb','1.0'), ('BioPerl','1.6.924','-Perl-5.22.1'), ('BLAST+','2.3.0', '-Python-2.7.11'), @@ -35,10 +32,10 @@ postinstallcmds = [ perlmajver = perlver.split('.')[0] sanity_check_paths = { - 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Algorithm/HMM.pm' % (perlmajver, perlver), - 'lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm' % (perlmajver, perlver)], - 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Algorithm/HMM' % (perlmajver, perlver), - 'lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Bio/Tools/PSort' % (perlmajver, perlver)], + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch index 77c77af3b7..4272ae4de8 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch @@ -1,3 +1,5 @@ +# Removed q and a and perl scripting environment set accordingly. +# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG) diff -ru bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm --- bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm 2010-07-29 00:12:43.000000000 +0200 +++ bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm 2015-11-26 13:50:18.000000000 +0100 diff --git a/easybuild/easyconfigs/p/pftools/pftools-V3-foss-2016a.eb b/easybuild/easyconfigs/p/pftools/pftoolsV3-24.03.16-foss-2016a.eb similarity index 76% rename from easybuild/easyconfigs/p/pftools/pftools-V3-foss-2016a.eb rename to easybuild/easyconfigs/p/pftools/pftoolsV3-24.03.16-foss-2016a.eb index e42e2a92c5..049184350c 100644 --- a/easybuild/easyconfigs/p/pftools/pftools-V3-foss-2016a.eb +++ b/easybuild/easyconfigs/p/pftools/pftoolsV3-24.03.16-foss-2016a.eb @@ -1,7 +1,7 @@ easyblock='ConfigureMake' -name = 'pftools' -version = 'V3' +name = 'pftoolsV3' +version = '24.03.16' homepage = 'http://web.expasy.org/pftools/' description = """The pftools package contains all the software necessary to build protein and DNA generalized profiles and use @@ -10,8 +10,9 @@ description = """The pftools package contains all the software necessary to buil toolchain = {'name': 'foss', 'version': '2016a'} -sources = ['%(name)s%(version)s.tar.gz'] -source_urls = ['ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/pftoolsV3/'] +sources = ['%(name)s.tar.gz'] +source_urls = ['ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/%(name)s/'] +checksums = ['ef1d3c7583d764cff06861fca75be455'] sanity_check_paths = { 'files': ['bin/ptof', 'bin/htop', 'bin/6ft', 'bin/2ft', 'bin/pfdump', 'bin/pfscan', 'bin/pfsearch'], -- GitLab From 055e2760207e51ed2491ab7fb3f703034e330539 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Jul 2016 18:32:31 +0200 Subject: [PATCH 078/701] version change, removed perlmajver --- .../p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 1 - ...-24.03.16-foss-2016a.eb => pftoolsV3-240316-foss-2016a.eb} | 4 ++-- 2 files changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/pftools/{pftoolsV3-24.03.16-foss-2016a.eb => pftoolsV3-240316-foss-2016a.eb} (94%) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index b74de25012..eb5d42321b 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -30,7 +30,6 @@ postinstallcmds = [ "cp -r psort/* %(installdir)s/.", ] -perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], diff --git a/easybuild/easyconfigs/p/pftools/pftoolsV3-24.03.16-foss-2016a.eb b/easybuild/easyconfigs/p/pftools/pftoolsV3-240316-foss-2016a.eb similarity index 94% rename from easybuild/easyconfigs/p/pftools/pftoolsV3-24.03.16-foss-2016a.eb rename to easybuild/easyconfigs/p/pftools/pftoolsV3-240316-foss-2016a.eb index 049184350c..2e4606fec1 100644 --- a/easybuild/easyconfigs/p/pftools/pftoolsV3-24.03.16-foss-2016a.eb +++ b/easybuild/easyconfigs/p/pftools/pftoolsV3-240316-foss-2016a.eb @@ -1,7 +1,7 @@ easyblock='ConfigureMake' name = 'pftoolsV3' -version = '24.03.16' +version = '240316' homepage = 'http://web.expasy.org/pftools/' description = """The pftools package contains all the software necessary to build protein and DNA generalized profiles and use @@ -19,4 +19,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' -- GitLab From c3e97c9ca2b89fcb1a5244b7e750831f5317fd9d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Jul 2016 18:37:38 +0200 Subject: [PATCH 079/701] version change for pftoolsV3 dep --- .../easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index eb5d42321b..6329945e3f 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -19,7 +19,7 @@ dependencies = [ ('libpsortb','1.0'), ('BioPerl','1.6.924','-Perl-5.22.1'), ('BLAST+','2.3.0', '-Python-2.7.11'), - ('pftools','2.3'), + ('pftoolsV3','240316'), ] options = {'modulename': 'Bio::Tools::PSort'} -- GitLab From 75aa60ab20fc40390e1a8089696b770fd089eac5 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Jul 2016 18:40:07 +0200 Subject: [PATCH 080/701] format of date --- .../easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- ...V3-240316-foss-2016a.eb => pftoolsV3-20160324-foss-2016a.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/pftools/{pftoolsV3-240316-foss-2016a.eb => pftoolsV3-20160324-foss-2016a.eb} (96%) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index 6329945e3f..ac9f122387 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -19,7 +19,7 @@ dependencies = [ ('libpsortb','1.0'), ('BioPerl','1.6.924','-Perl-5.22.1'), ('BLAST+','2.3.0', '-Python-2.7.11'), - ('pftoolsV3','240316'), + ('pftoolsV3','20160324'), ] options = {'modulename': 'Bio::Tools::PSort'} diff --git a/easybuild/easyconfigs/p/pftools/pftoolsV3-240316-foss-2016a.eb b/easybuild/easyconfigs/p/pftools/pftoolsV3-20160324-foss-2016a.eb similarity index 96% rename from easybuild/easyconfigs/p/pftools/pftoolsV3-240316-foss-2016a.eb rename to easybuild/easyconfigs/p/pftools/pftoolsV3-20160324-foss-2016a.eb index 2e4606fec1..8d5302dd6c 100644 --- a/easybuild/easyconfigs/p/pftools/pftoolsV3-240316-foss-2016a.eb +++ b/easybuild/easyconfigs/p/pftools/pftoolsV3-20160324-foss-2016a.eb @@ -1,7 +1,7 @@ easyblock='ConfigureMake' name = 'pftoolsV3' -version = '240316' +version = '20160324' homepage = 'http://web.expasy.org/pftools/' description = """The pftools package contains all the software necessary to build protein and DNA generalized profiles and use -- GitLab From 373a99195778daa2a3345ade490f2b0aa0d8d044 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 13 Jul 2016 19:09:20 +0200 Subject: [PATCH 081/701] sanity check paths --- easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb index 8f16d58e42..1613e1f3c8 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb @@ -17,4 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic --disable-cpp --enable-jit" -moduleclass = 'devel' +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "libpcre2-8.a"], + 'dirs': [], +} + +moduleclass = 'devel' \ No newline at end of file -- GitLab From 723cfd1965fedc9e90e4f38c2b51aa84501857ed Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 14 Jul 2016 14:37:22 +0200 Subject: [PATCH 082/701] Trinity with foss 2016a --- .../t/Trinity/Trinity-2.2.0-foss-2016a.eb | 41 +++++++++++++++++++ .../Trinity-2.2.0_jellyfish-Makefile.patch | 30 ++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.2.0_jellyfish-Makefile.patch diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000..1b99713c8c --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb @@ -0,0 +1,41 @@ +# 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 = 'Trinity' +version = '2.2.0' + +homepage = 'http://trinityrnaseq.github.io/' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'chrysalis_commandline_noconsts_2012-10-05.patch', + 'Trinity-2.2.0_jellyfish-Makefile.patch', +] + +builddependencies = [ + ('Autotools', '20150215'), +] + +java = 'Java' +javaver = '1.8.0_92' + +dependencies = [ + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-%s-%s' % (java, javaver), True), + ('Bowtie', '1.1.2'), + ('Bowtie2', '2.2.8'), + ('ncurses', '6.0',), + ('zlib', '1.2.8'), + ('Perl', '5.22.1'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0_jellyfish-Makefile.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0_jellyfish-Makefile.patch new file mode 100644 index 0000000000..33fecc0911 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0_jellyfish-Makefile.patch @@ -0,0 +1,30 @@ +use EasyBuild-provided zlib, don't hardcode gcc/g++ for jellyfish plugin +authors: B. Hajgato (Vrije Universiteit Brussel), Kenneth Hoste (HPC-UGent) +--- trinityrnaseq-2.2.0/trinity-plugins/Makefile.orig 2016-07-07 11:42:18.000000000 +0200 ++++ trinityrnaseq-2.2.0/trinity-plugins/Makefile 2016-07-07 11:44:04.000000000 +0200 +@@ -2,6 +2,9 @@ + JELLYFISH_CODE="jellyfish-2.1.4" + HTSLIB_CODE="htslib.github.Aug182015.tar.gz" + ++CC?=gcc ++CXX?=g++ ++ + ####################### + ### Required by Trinity + ####################### +@@ -26,12 +29,13 @@ + + samtools: + tar xvf samtools-0.1.19.tar.bz2 +- cd samtools-0.1.19 && $(MAKE) ${LTINFO} ++ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i samtools-0.1.19/misc/Makefile ++ cd samtools-0.1.19 && $(MAKE) LIBPATH=-L${EBROOTZLIB}/lib + mv samtools-0.1.19/samtools ./BIN/. + + jellyfish: + tar -zxvf ${JELLYFISH_CODE}.tar.gz && ln -sf ${JELLYFISH_CODE} tmp.jellyfish +- cd ./tmp.jellyfish/ && ./configure CC=gcc CXX=g++ --enable-static --disable-shared --prefix=`pwd` && $(MAKE) LDFLAGS="-lpthread -all-static" AM_CPPFLAGS="-Wall -Wnon-virtual-dtor -I"`pwd`"/include" ++ cd ./tmp.jellyfish/ && ./configure CC=$(CC) CXX=$(CXX) --enable-static --disable-shared --prefix=`pwd` && $(MAKE) LDFLAGS="-lpthread -all-static" AM_CPPFLAGS="-Wall -Wnon-virtual-dtor -I"`pwd`"/include" + mv tmp.jellyfish jellyfish + + htslib_target: -- GitLab From 0a772d2e45601c2586924cd8bab9da35453f840f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 14 Jul 2016 18:36:37 +0200 Subject: [PATCH 083/701] GST-plugins with foss2016a --- .../cairo-1.14.6-foss-2016a-GLib-2.48.0.eb | 53 +++++++++++++++++++ ...GObject-Introspection-1.48.0-foss-2016a.eb | 48 +++++++++++++++++ .../GST-plugins-base-1.9.1-foss-2016a.eb | 42 +++++++++++++++ .../g/GStreamer/GStreamer-1.9.1-foss-2016a.eb | 38 +++++++++++++ 4 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.9.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..d3ff41d3f3 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' +glibver = '2.48.0' +versionsuffix = '-GLib-%s' % glibver + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.3'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.95'), + ('expat', '2.1.1'), + ('GLib', glibver), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] +builddependencies = [ + ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb new file mode 100644 index 0000000000..e8ddb76e89 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.48.0' + +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': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('Python', '2.7.11'), + ('GLib', glibver), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6', '-GLib-%s' % glibver), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +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'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb new file mode 100644 index 0000000000..34dd19beae --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '1.9.1' + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GStreamer', '1.9.1'), + ('Automake', '1.15'), + ('Autoconf', '2.69'), + ('gettext', '0.19.7'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('XZ', '5.2.2'), + ('libtool', '2.4.6'), + ('pkgconfig', '1.1.0', '-Python-2.7.11'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) 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-1.9.1-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.9.1-foss-2016a.eb new file mode 100644 index 0000000000..6fb42440e5 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.9.1-foss-2016a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '1.9.1' + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0'), + ('zlib', '1.2.8'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '3.0.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From 9b5a7271b8f67280599be002f49adbb91392d4f2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 14 Jul 2016 20:30:50 +0200 Subject: [PATCH 084/701] GLib dep down, order matters --- .../easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb index d3ff41d3f3..9259854841 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb @@ -23,13 +23,13 @@ dependencies = [ ('pixman', '0.34.0'), ('fontconfig', '2.11.95'), ('expat', '2.1.1'), - ('GLib', glibver), ('libX11', '1.6.3'), ('libxcb', '1.11.1'), ('libXrender', '0.9.9'), ('libXext', '1.3.3'), ('libXau', '1.0.8'), ('libXdmcp', '1.1.2'), + ('GLib', glibver), ] builddependencies = [ ('renderproto', '0.11'), -- GitLab From 6fee974e4d050782c5f52c95f72abb566a5f12b7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 14 Jul 2016 20:38:28 +0200 Subject: [PATCH 085/701] GConf with foss2016a --- .../d/DBus/DBus-1.10.8-foss-2016a.eb | 24 ++++++++++++ .../d/dbus-glib/dbus-glib-0.106-foss-2016a.eb | 25 ++++++++++++ .../g/GConf/GConf-3.2.6-foss-2016a.eb | 39 +++++++++++++++++++ 3 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb new file mode 100644 index 0000000000..0940c66fb5 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.10.8' + +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': 'foss', 'version': '2016a'} + +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', SHLIB_EXT]], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb new file mode 100644 index 0000000000..3a355efc71 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.106' + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('DBus', '1.10.8'), + ('expat', '2.2.0'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb new file mode 100644 index 0000000000..6b42d8e1b6 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('dbus-glib', '0.106'), + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0'), + ('libxml2', '2.9.3'), + ('GTK+', '2.24.30'), + ('intltool', '0.51.0', '-Perl-5.22.1'), +] + +configopts = '--disable-orbit ' + +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' -- GitLab From bcce53e26ab921aa30ccfb7582ce0ce8e30f1b4e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 14 Jul 2016 21:05:02 +0200 Subject: [PATCH 086/701] wxPython with foss2016a --- ...Python-3.0.2.0-foss-2016a-Python-2.7.11.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0b548d2bb7 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,37 @@ +name = 'wxPython' +version = '3.0.2.0' +versionsuffix = "-Python-%(pyver)s" + +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': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] + +#patches = ['%(name)s_%(version)s_intel.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), + ('expat', '2.2.0'), + ('GTK+', '2.24.30'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '1.9.1'), + + ('libGLU', '9.0.0', '-Mesa-11.2.1'), + ('libSM', '1.2.2'), + ('libXxf86vm', '1.1.4'), +] +# ('Mesa', '11.2.1'), +moduleclass = 'vis' + -- GitLab From 70efaeceabf889e02fc2d15c058d026e9aa75c97 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 14 Jul 2016 21:18:42 +0200 Subject: [PATCH 087/701] XZ with gettext 0.19.7 --- .../easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb | 2 +- .../g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb index 9259854841..cdfa7fd0c2 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('freetype', '2.6.3'), ('pixman', '0.34.0'), ('fontconfig', '2.11.95'), - ('expat', '2.1.1'), + ('expat', '2.2.0'), ('libX11', '1.6.3'), ('libxcb', '1.11.1'), ('libXrender', '0.9.9'), diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb index 34dd19beae..16d3c00dec 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb @@ -21,9 +21,8 @@ dependencies = [ ('gettext', '0.19.7'), ] -# does not work with Bison 3.x builddependencies = [ - ('XZ', '5.2.2'), + ('XZ', '5.2.2', '-gettext-0.19.7'), ('libtool', '2.4.6'), ('pkgconfig', '1.1.0', '-Python-2.7.11'), ] -- GitLab From d686d4752a27ea7c9a3b4247e72f8baf7016559d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 14 Jul 2016 21:30:01 +0200 Subject: [PATCH 088/701] removed comments --- .../w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb index 0b548d2bb7..21c40b17c6 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb @@ -15,8 +15,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-src-%(version)s.tar.bz2'] -#patches = ['%(name)s_%(version)s_intel.patch'] - dependencies = [ ('Python', '2.7.11'), ('libpng', '1.6.21'), @@ -27,11 +25,10 @@ dependencies = [ ('GTK+', '2.24.30'), ('GConf', '3.2.6'), ('GST-plugins-base', '1.9.1'), - ('libGLU', '9.0.0', '-Mesa-11.2.1'), ('libSM', '1.2.2'), ('libXxf86vm', '1.1.4'), ] -# ('Mesa', '11.2.1'), + moduleclass = 'vis' -- GitLab From 31fd5d1a134c0192da73b4a03eae04164191d03f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 14 Jul 2016 21:30:57 +0200 Subject: [PATCH 089/701] newline removed --- .../w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb index 21c40b17c6..abb19d3368 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb @@ -31,4 +31,3 @@ dependencies = [ ] moduleclass = 'vis' - -- GitLab From fa2734e1839715390b8996b50d571f150d8f30fd Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 15 Jul 2016 13:24:22 +0200 Subject: [PATCH 090/701] BayeScan-2.1 for foss-2016a --- .../b/BayeScan/BayeScan-2.1-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb new file mode 100644 index 0000000000..fe025c2502 --- /dev/null +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BayeScan' +version = '2.1' + +homepage = 'http://cmpg.unibe.ch/software/BayeScan/' +description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, + using differences in allele frequencies between populations.""" + +# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/'] +sources = ['%(name)s%(version)s.zip'] + +prebuildopts = "sed -i .bk 's/g\+\+/${CC} ${CFLAGS}/g' Makefile && " + +start_dir = 'source' + +files_to_copy = [(['source/bayescan_%(version)s'], 'bin'), 'BayeScan%(version)s_manual.pdf' , 'input_examples', 'R functions'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/bayescan_%(version)s'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 44e0abbd3bd32de52ad77f21100b1a8cca291141 Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 15 Jul 2016 13:24:41 +0200 Subject: [PATCH 091/701] remove space before suffix in sed command --- easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb index fe025c2502..438b382f2b 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb @@ -19,7 +19,7 @@ toolchainopts = {'openmp': True} source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/'] sources = ['%(name)s%(version)s.zip'] -prebuildopts = "sed -i .bk 's/g\+\+/${CC} ${CFLAGS}/g' Makefile && " +prebuildopts = "sed -i.bk 's/g\+\+/${CC} ${CFLAGS}/g' Makefile && " start_dir = 'source' -- GitLab From 2492f018ab8dea0dccb92e4134ad4a2b2f6f0fea Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 15 Jul 2016 13:34:11 +0200 Subject: [PATCH 092/701] fix sed command, use CXX and CXXFLAGS instead of CC and CFLAGS --- easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb index 438b382f2b..572719879c 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb @@ -19,7 +19,7 @@ toolchainopts = {'openmp': True} source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/'] sources = ['%(name)s%(version)s.zip'] -prebuildopts = "sed -i.bk 's/g\+\+/${CC} ${CFLAGS}/g' Makefile && " +prebuildopts = "sed -i.bk 's/g++/${CXX} ${CXXFLAGS}/g' Makefile && " start_dir = 'source' -- GitLab From f7c9b23ba2cf1b06e32f446c996ecf6d31324db8 Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 15 Jul 2016 14:29:48 +0200 Subject: [PATCH 093/701] version 6.1.1 with foss 2016a --- .../e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb new file mode 100644 index 0000000000..fc1815fa18 --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Provided binaries required OpenBLAS and GSL libraries + +easyblock = 'MakeCp' + +name = 'EIGENSOFT' +version = '6.1.1' + +homepage = 'http://www.hsph.harvard.edu/alkes-price/software/' +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) + and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components + analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; + the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, + minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in + plotting script and supports multiple file formats and quantitative phenotypes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/', + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/'] +sources = ['EIG%(version)s.tar.gz'] + +dependencies = [ + ('GSL', '2.1'), +] + +# -lm and -pthread are missing in the Makefile +buildopts = 'LDLIBS="-lgsl -lopenblas -lgfortran -lrt -lm" LDFLAGS="-pthread"' + +start_dir = 'src' + +files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c7f520aeb9493f979c59c071c77e66b9d2ec0552 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 15 Jul 2016 15:19:25 +0200 Subject: [PATCH 094/701] {phys}[intel-2015b] Yambo 4.0.2 with QuantumESPRESSO-5.2.1 (REVIEW) --- ...ev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb new file mode 100644 index 0000000000..87a12819cd --- /dev/null +++ b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb @@ -0,0 +1,52 @@ +easyblock = 'MakeCp' + +name = 'Yambo' +version = '4.0.2-rev.90' +qe = 'QuantumESPRESSO' +qever = '5.2.1' +versionsuffix = '%s-%s' % (qe, qever) + +homepage = 'http://www.yambo-code.org' +description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. + Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://qe-forge.org/gf/download/frsrelease/201/870/'] +checksums = ['03d5ffc655eb4c03db4e264606117c86'] + +dependencies = [ + ('netCDF-Fortran', '4.4.2'), + (qe, qever), +] + +with_configure = 'True' + +configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" ' +#configopts = 'CC=$CC_SEQ MPICC=$CC CPPFLAGS="" FCFLAGS="-nofor_main" ' +configopts += '--with-blas-libs="$LIBBLAS" ' +configopts += '--with-lapack-libs="$LIBLAPACK" ' +configopts += '--with-fft-libs="$LIBFFT" ' +configopts += '--with-iotk-path="$EBROOTQUANTUMESPRESSO/espresso-%s/S3DE/iotk" ' % qever +configopts += '--enable-netcdf-hdf5 ' +configopts += '--with-netcdf-includedir="$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libdir="$EBROOTNETCDFMINFORTRAN/lib" ' + +buildopts = 'yambo interfaces ypp' + +parallel = 1 + +files_to_copy = [(['bin/*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/'+prog for prog in ['a2y', 'p2y', 'yambo', 'ypp' ]], + 'dirs': [] +} + +#modextraline = { +# "remove-path" : "PATH $::env(EBROOTQUANTUMESPRESSO)/expresso-%s/YAMBO/bin" % qever +#} + +moduleclass = 'phys' -- GitLab From 0bc6dd8e219da087ca8c7234cd023755fa1e5eed Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 15 Jul 2016 15:22:42 +0200 Subject: [PATCH 095/701] run make install after make --- easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb index fc1815fa18..6cc874f0c9 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb @@ -30,7 +30,7 @@ dependencies = [ ] # -lm and -pthread are missing in the Makefile -buildopts = 'LDLIBS="-lgsl -lopenblas -lgfortran -lrt -lm" LDFLAGS="-pthread"' +buildopts = 'LDLIBS="-lgsl -lopenblas -lgfortran -lrt -lm" LDFLAGS="$LDFLAGS -pthread" && make install' start_dir = 'src' -- GitLab From e9301e83dc5c00553f55aa00775fa8a6f16edbec Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 15 Jul 2016 15:23:04 +0200 Subject: [PATCH 096/701] version 6.0.1 --- .../e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb new file mode 100644 index 0000000000..36fcca43b8 --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Provided binaries required OpenBLAS and GSL libraries + +easyblock = 'MakeCp' + +name = 'EIGENSOFT' +version = '6.0.1' + +homepage = 'http://www.hsph.harvard.edu/alkes-price/software/' +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) + and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components + analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; + the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, + minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in + plotting script and supports multiple file formats and quantitative phenotypes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/', + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/'] +sources = ['EIG%(version)s.tar.gz'] + +dependencies = [ + ('GSL', '2.1'), +] + +# -lm and -pthread are missing in the Makefile +# also run "make install" after make to copy all binaries to the bin dir +buildopts = 'LDLIBS="-lgsl -lopenblas -lgfortran -lrt -lm" LDFLAGS="$LDFLAGS -pthread" && make install' + +start_dir = 'src' + +files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 2f3326c46b9a5f560d1bc0646f19e55267b235f9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 15 Jul 2016 15:27:54 +0200 Subject: [PATCH 097/701] added - --- .../Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb index 87a12819cd..ee90e72808 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb @@ -4,7 +4,7 @@ name = 'Yambo' version = '4.0.2-rev.90' qe = 'QuantumESPRESSO' qever = '5.2.1' -versionsuffix = '%s-%s' % (qe, qever) +versionsuffix = '-%s-%s' % (qe, qever) homepage = 'http://www.yambo-code.org' description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. -- GitLab From c840c8745da4a8271b555161e35cb700b5308161 Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 15 Jul 2016 15:30:51 +0200 Subject: [PATCH 098/701] made lines shorter than 120 chars --- .../e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb | 12 ++++++------ .../e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb index 36fcca43b8..91d5649298 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb @@ -11,12 +11,12 @@ name = 'EIGENSOFT' version = '6.0.1' homepage = 'http://www.hsph.harvard.edu/alkes-price/software/' -description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) - and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components - analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; - the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, - minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in - plotting script and supports multiple file formats and quantitative phenotypes.""" +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. +2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal +components analysis to explicitly model ancestry differences between cases and controls along continuous axes of +variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT +package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb index 6cc874f0c9..9d605117a0 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb @@ -11,12 +11,12 @@ name = 'EIGENSOFT' version = '6.1.1' homepage = 'http://www.hsph.harvard.edu/alkes-price/software/' -description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) - and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components - analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; - the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, - minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in - plotting script and supports multiple file formats and quantitative phenotypes.""" +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. +2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal +components analysis to explicitly model ancestry differences between cases and controls along continuous axes of +variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT +package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" toolchain = {'name': 'foss', 'version': '2016a'} -- GitLab From b58a99e984a0ed7134cc632dd7013fe3e211ce78 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 18 Jul 2016 17:20:51 +0800 Subject: [PATCH 099/701] add easyconfig pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb, add easyconfig spglib-1.9.4.2-intel-2016b-Python-2.7.12.eb --- ...ymatgen-4.1.1-intel-2016b-Python-2.7.12.eb | 26 +++++++++++++++++++ ...pglib-1.9.4.2-intel-2016b-Python-2.7.12.eb | 24 +++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.9.4.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..21004fbe46 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '4.1.1' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('spglib', '1.9.4.2', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.4.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/spglib/spglib-1.9.4.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9a2186080b --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.9.4.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'spglib' +version = '1.9.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' -- GitLab From 430e9e87c326d38fdf3161e1784a4af131c37a28 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 18 Jul 2016 11:50:01 +0200 Subject: [PATCH 100/701] Java dep, Perl dep --- ...LAST-2.3.1-foss-2016a-Java-1.8.0_92-Perl-5.22.1.eb} | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/p/PLAST/{PLAST-2.3.1-foss-2016a.eb => PLAST-2.3.1-foss-2016a-Java-1.8.0_92-Perl-5.22.1.eb} (73%) diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92-Perl-5.22.1.eb similarity index 73% rename from easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb rename to easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92-Perl-5.22.1.eb index 1baf1e7347..290a7183f9 100644 --- a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92-Perl-5.22.1.eb @@ -2,6 +2,7 @@ easyblock = 'CMakeMake' name = 'PLAST' version = '2.3.1' +versionsuffix = '-Java-%(javaver)s-Perl-%(perlver)s' homepage = "http://www.irisa.fr/symbiose/projects/plast/" description = """PLAST is a parallel alignment search tool for comparing large protein banks""" @@ -11,7 +12,14 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/PLAST-software/plast-library/releases/download/v%(version)s/'] sources=['%(namelower)s_source_v%(version)s.tar.gz'] -builddependencies = [('CMake', '3.5.2')] +builddependencies = [ + ('CMake', '3.5.2') +] + +dependencies = [ + ('Java', '1.8.0_92', '', True), + ('Perl', '5.22.1') +] sanity_check_paths = { 'files': [], -- GitLab From 8fea05242806ca5480f701c73b38f14b58fcbf56 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 Jul 2016 13:43:06 +0200 Subject: [PATCH 101/701] remove-path added --- .../Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb index ee90e72808..9267180d04 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb @@ -45,8 +45,6 @@ sanity_check_paths = { 'dirs': [] } -#modextraline = { -# "remove-path" : "PATH $::env(EBROOTQUANTUMESPRESSO)/expresso-%s/YAMBO/bin" % qever -#} +modtclfooter = "remove-path PATH $::env(EBROOTQUANTUMESPRESSO)/espresso-%s/YAMBO/bin" % qever moduleclass = 'phys' -- GitLab From c31a43d0b17eb8f06f651beee0e4205fdfd35c98 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 20 Jul 2016 14:20:53 +0200 Subject: [PATCH 102/701] foss 2016a versions of scikit-learn for both Python 2.7.11 and 3.5.1 --- ...t-learn-0.17.1-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ ...it-learn-0.17.1-foss-2016a-Python-3.5.1.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..7a34f126ed --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.17.1' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..9c2111d946 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.17.1' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 8fcc5f377d76f3e97a988cb1dd68776539ade22e Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Thu, 21 Jul 2016 15:50:59 +0200 Subject: [PATCH 103/701] GStreamer 1.6.4 using the foss 2016a toolchain and the base plugins. --- .../GST-plugins-base-1.6.4-foss-2016a.eb | 34 ++++++++++++++++ .../g/GStreamer/GStreamer-1.6.4-foss-2016a.eb | 39 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb new file mode 100644 index 0000000000..6d1390515a --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '1.6.4' + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '1.6.4')] + +builddependencies = [ + ('Bison', '3.0.4', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) 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-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb new file mode 100644 index 0000000000..05dfd4ddef --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '1.6.4' + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('Bison', '3.0.4', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['reamer', 'base', + 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From 4f88a211b1ec32f12a8342ff143d015039db6db8 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 25 Jul 2016 13:26:06 +1200 Subject: [PATCH 104/701] Upgrade paths to licence files --- easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb | 3 +-- .../easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb | 3 +-- .../m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb | 3 +-- .../m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb | 3 +-- 4 files changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb b/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb index 519d0887cc..de8bfef38e 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb @@ -11,7 +11,6 @@ toolchainopts = {'usempi': True} sources = ['%(namelower)s.%(version)s.tar.gz'] # license file -import os -license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') +license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb index 25842fde1c..c80d4d1ee1 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb @@ -15,7 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#import os -#license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') +#license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb index 3d1681fc2e..251958da52 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb @@ -15,7 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#import os -#license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') +#license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb index 119e4e7dfb..47852f7b9a 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb @@ -15,7 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#import os -#license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') +#license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' -- GitLab From 30aeff37fd7f644e76061214cb1d5e6cb248dc7e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 26 Jul 2016 23:40:05 +0800 Subject: [PATCH 105/701] modify easyconfig VASP-5.4.1-intel-2016.02-GCC-4.9.eb --- .../easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 2a6923ac23..0a9a899dd9 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -19,10 +19,13 @@ prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' # path to libfftw3xf_intel.a is hardcoded in makefile.include prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$(FFTW_LIB_DIR)|" makefile.include && ' +# we use static mkl later +prebuildopts += 'sed -i "s|-mkl||" makefile.include && ' + # VASP uses LIBS as a list of folders prebuildopts += 'unset LIBS && ' -buildopts = 'all BLACS="$LIBBLACS" ' +buildopts = 'all BLACS="$LIBBLACS" SCALAPACK="$LIBSCALAPACK"' parallel = 1 -- GitLab From aff1236e8eed94622c55e200981b6abfaa31aec3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 27 Jul 2016 13:22:46 +0200 Subject: [PATCH 106/701] Sphinx with foss2016a --- .../Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb | 76 +++++++++++++++++++ .../Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb | 76 +++++++++++++++++++ 2 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..582ea20b96 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,76 @@ +# Dependency for OBITools. +easyblock = 'Bundle' + +name = 'Sphinx' +version = '1.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('Pygments', '2.1.3', '-Python-%(pyver)s'), + ('requests', '2.10.0', versionsuffix), +] + + +exts_list = [ + ('imagesize', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.io/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Docutils', '0.12', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + }), + ('Babel', '2.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + ('alabaster', '0.7.8', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + }), + # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work + ('sphinx_rtd_theme', '0.1.10a0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + }), +] + +# Tests below do not work since pdflatex is installed in OS. +# Sphinx unit tests *after* installing extensions +# postinstallcmds = [' && '.join([ +# "cd %(builddir)s/%(name)s/%(name)s-%(version)s/", +# "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages/:$PYTHONPATH make test", +# ])] + +# 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/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..bd70bc9c30 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,76 @@ +# Dependency for OBITools. +easyblock = 'Bundle' + +name = 'Sphinx' +version = '1.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.1'), + ('Pygments', '2.1.3', '-Python-%(pyver)s'), + ('requests', '2.10.0', versionsuffix), +] + + +exts_list = [ + ('imagesize', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.io/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Docutils', '0.12', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + }), + ('Babel', '2.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + ('alabaster', '0.7.8', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + }), + # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work + ('sphinx_rtd_theme', '0.1.10a0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + }), +] + +# Tests below do not work since pdflatex is installed in OS. +# Sphinx unit tests *after* installing extensions +# postinstallcmds = [' && '.join([ +# "cd %(builddir)s/%(name)s/%(name)s-%(version)s/", +# "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages/:$PYTHONPATH make test", +# ])] + +# 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/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From f92e12c843b0efff1b089bf044ec934335d8ec49 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 27 Jul 2016 13:25:31 +0200 Subject: [PATCH 107/701] Sphinx with foss2016a --- .../Pygments-2.1.3-foss-2016a-Python-3.5.1.eb | 26 +++++++++++++++++++ ...requests-2.10.0-foss-2016a-Python-3.5.1.eb | 24 +++++++++++++++++ .../Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb | 9 +++---- .../Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb | 9 +++---- 4 files changed, 58 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..d1cd521edb --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + + +dependencies = [ + ('Python', '3.5.1'), +] + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..1435fab7e5 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests/%(version)s' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/requests-%(version)s-py%(pyshortver)s.egg'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb index 582ea20b96..5aa84bbcef 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb @@ -56,12 +56,11 @@ exts_list = [ }), ] -# Tests below do not work since pdflatex is installed in OS. # Sphinx unit tests *after* installing extensions -# postinstallcmds = [' && '.join([ -# "cd %(builddir)s/%(name)s/%(name)s-%(version)s/", -# "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages/:$PYTHONPATH make test", -# ])] +postinstallcmds = [' && '.join([ + "cd %(builddir)s/%(name)s/%(name)s-%(version)s/", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages/:$PYTHONPATH make test", +])] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb index bd70bc9c30..162f5af933 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb @@ -56,12 +56,11 @@ exts_list = [ }), ] -# Tests below do not work since pdflatex is installed in OS. # Sphinx unit tests *after* installing extensions -# postinstallcmds = [' && '.join([ -# "cd %(builddir)s/%(name)s/%(name)s-%(version)s/", -# "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages/:$PYTHONPATH make test", -# ])] +postinstallcmds = [' && '.join([ + "cd %(builddir)s/%(name)s/%(name)s-%(version)s/", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages/:$PYTHONPATH make test", +])] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -- GitLab From b66042605b1b69e8816e53e4c99f58f3df163c75 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 27 Jul 2016 13:30:28 +0200 Subject: [PATCH 108/701] Theano with foss2016a --- .../Theano-0.8.2-foss-2016a-Python-2.7.11.eb | 29 +++++++++++++++++++ .../Theano-0.8.2-foss-2016a-Python-3.5.1.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..f9de6cacae --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('binutils', '2.25', '', ('GCCcore','4.9.3')), + ('Pygments', '2.1.3', versionsuffix), + ('Sphinx', '1.4.5', versionsuffix) +] + +sanity_check_paths = { + 'files': ['bin/theano-cache', + 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': [] +} + +moduleclass = 'math' \ No newline at end of file diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..7049aceac7 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('binutils', '2.25', '', ('GCCcore','4.9.3')), + ('Pygments', '2.1.3', versionsuffix), + ('Sphinx', '1.4.5', versionsuffix) +] + +sanity_check_paths = { + 'files': ['bin/theano-cache', + 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': [] +} + +moduleclass = 'math' \ No newline at end of file -- GitLab From a224a61018c32f26e7d525a8079009a067fde72e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 27 Jul 2016 13:38:01 +0200 Subject: [PATCH 109/701] Removed comment --- .../s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb | 1 - .../easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb index 5aa84bbcef..edf98e8d1e 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb @@ -1,4 +1,3 @@ -# Dependency for OBITools. easyblock = 'Bundle' name = 'Sphinx' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb index 162f5af933..f608175b73 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb @@ -1,4 +1,3 @@ -# Dependency for OBITools. easyblock = 'Bundle' name = 'Sphinx' -- GitLab From 877960f23683089a352eddb90a27127e826f8bbd Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 27 Jul 2016 14:05:31 +0200 Subject: [PATCH 110/701] version 3.7.2 -> 3.7.3 --- ...a-Python-2.7.11.eb => PETSc-3.7.3-foss-2016a-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.2-foss-2016a-Python-2.7.11.eb => PETSc-3.7.3-foss-2016a-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.2-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb -- GitLab From 509e62930698f749229af31253e522095c6455bb Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 Aug 2016 12:01:41 +0800 Subject: [PATCH 111/701] include official patches --- .../v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 0a9a899dd9..29745c333e 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -14,6 +14,14 @@ toolchainopts = {'usempi': True} # Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code sources = [SOURCELOWER_TAR_GZ] +patches = ['patch.5.4.1.08072015', 'patch.5.4.1.27082015', 'patch.5.4.1.06112015'] + +checksums = ['57c2b07d0f70987000033984e913f1a6', # vasp.5.4.1.tar.gz + 'ee242452bba6bb37459745f4617649d7', # patch.5.4.1.08072015 + 'b137eb13804a60df382e77495dc738f9', # patch.5.4.1.27082015 + 'd64b8f0ae861db7a76e6e9c9ffa188a1', # patch.5.4.1.06112015 + ] + prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' # path to libfftw3xf_intel.a is hardcoded in makefile.include -- GitLab From bc51aadc39dd66714907009f40a1c2a58024ec56 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Aug 2016 12:24:27 +0200 Subject: [PATCH 112/701] {geo}[foss-2016a] pyGIMLi - Python 3.5.1 (REVIEW) --- .../c/CastXML/CastXML-d5934bd-foss-2016a.eb | 32 +++++++++ .../c/CppUnit/CppUnit-1.12.1-foss-2016a.eb | 19 ++++++ ...pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb | 68 +++++++++++++++++++ .../p/pyGIMLi/pyGIMLi-a190c53_openblas.patch | 13 ++++ ...ygccxml-648e8da-foss-2016a-Python-3.5.1.eb | 30 ++++++++ ...us-2c6c05b7a7d2-foss-2016a-Python-3.5.1.eb | 32 +++++++++ .../t/Triangle/Triangle-1.6-foss-2016a.eb | 34 ++++++++++ .../t/Triangle/Triangle-1.6_makefile.patch | 41 +++++++++++ 8 files changed, 269 insertions(+) create mode 100644 easybuild/easyconfigs/c/CastXML/CastXML-d5934bd-foss-2016a.eb create mode 100644 easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53_openblas.patch create mode 100644 easybuild/easyconfigs/p/pygccxml/pygccxml-648e8da-foss-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/p/pyplusplus/pyplusplus-2c6c05b7a7d2-foss-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6-foss-2016a.eb create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6_makefile.patch diff --git a/easybuild/easyconfigs/c/CastXML/CastXML-d5934bd-foss-2016a.eb b/easybuild/easyconfigs/c/CastXML/CastXML-d5934bd-foss-2016a.eb new file mode 100644 index 0000000000..c326e59979 --- /dev/null +++ b/easybuild/easyconfigs/c/CastXML/CastXML-d5934bd-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CastXML' +#latest Git commit was: +version = 'd5934bd' + +homepage = 'https://github.com/CastXML/CastXML' +description = """CastXML is a C-family abstract syntax tree XML output tool.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +#Only git repository: git clone https://github.com/CastXML/CastXML.git +sources = [SOURCE_TBZ2] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('Clang', '3.7.1'), + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/castxml"], + 'dirs': ["share/castxml"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-foss-2016a.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-foss-2016a.eb new file mode 100644 index 0000000000..f0709a3154 --- /dev/null +++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'CppUnit' +version = '1.12.1' + +homepage = 'http://sourceforge.net/projects/cppunit/' +description = """CppUnit is the C++ port of the famous JUnit framework for unit testing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, 'lib/pkgconfig/cppunit.pc'], + 'dirs': ['bin', 'include/cppunit', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..6bf2fcfe65 --- /dev/null +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,68 @@ +easyblock = 'CMakeMake' + +name = 'pyGIMLi' +#latest Git commit was: +version = 'a190c53' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pygimli.org/' +description = """pyGIMLi is an open-source multi-method library for solving inverse + and forward tasks related to geophysical problems. Written in C++ and Python, + it offers both efficiency and flexibility allowing you to quickly build + your own robust inversion applications for the geophysical problem at hand.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +#Only git repository: git clone https://github.com/gimli-org/gimli.git a190c53 +sources = [SOURCE_TBZ2] + +patches = ['%(name)s-%(version)s_openblas.patch'] + +#pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus +#Check scripts/buildThirdParty.sh +builddependencies = [ + ('CMake', '3.4.3'), + ('CastXML', 'd5934bd'), + ('pygccxml', '648e8da', '-Python-%(pyver)s'), + ('pyplusplus', '2c6c05b7a7d2', '-Python-%(pyver)s'), +] + +dependencies = [ + ('Python', '3.5.1'), + ('matplotlib', '1.5.1', '-Python-%(pyver)s'), + ('Clang', '3.7.1'), + ('Boost', '1.60.0', '-Python-%(pyver)s'), + ('zlib', '1.2.8'), + ('Triangle', '1.6'), + ('CppUnit', '1.12.1'), + ('SuiteSparse', '4.5.3', '-METIS-5.1.0'), +] + +separate_build_dir = True + +configopts = '-DBOOST_ROOT=$EBROOTBOOST ' +configopts += '-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.so ' +configopts += '-DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.so ' +configopts += '-DCASTXML_EXECUTABLE=$EBROOTCASTXML/bin/castxml ' +configopts += '-DPYGCCXML_PATH=$EBROOTPYGCCXML/lib/python%(pyshortver)s/site-packages/ ' +configopts += '-DPYPLUSPLUS_PATH=$EBROOTPYPLUSPLUS/lib/python%(pyshortver)s/site-packages/ ' + +buildopts = 'gimli pygimli apps' + +preinstallopts = 'mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages ' +preinstallopts += '&& cp -a ../gimli/python/. %(installdir)s/lib/python%(pyshortver)s/site-packages ' +preinstallopts += '&& cp -a ../easybuild_obj/lib/. %(installdir)s/lib/ ' +preinstallopts += '&& mkdir %(installdir)s/bin ' +preinstallopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin ||' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bms2vtk', 'dc1dinv', 'dc1dsmooth', 'fdem1dinv', 'fdem1dsmooth', + 'harmfit', 'invlinearmat', 'mrs1dblock', 'mrs1dsmooth', + 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']]+ + ['lib/libgimli.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/pygimli.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53_openblas.patch b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53_openblas.patch new file mode 100644 index 0000000000..b8d7de57ef --- /dev/null +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53_openblas.patch @@ -0,0 +1,13 @@ +# OpenBLAS cblas.h is loacted at include/cblas.h and not include/openblas/cblas.h +# Aug 04th 2016 by B. Hajgato (Free University Brussels - VUB) +--- gimli/src/gimli.cpp.orig 2016-08-04 08:53:28.000000000 +0200 ++++ gimli/src/gimli.cpp 2016-08-04 14:19:26.570541693 +0200 +@@ -28,7 +28,7 @@ + #include + + #if OPENBLAS_FOUND && !CONDA_BUILD +- #include ++ #include + // #else + // #include + #endif diff --git a/easybuild/easyconfigs/p/pygccxml/pygccxml-648e8da-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pygccxml/pygccxml-648e8da-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..fe4101769f --- /dev/null +++ b/easybuild/easyconfigs/p/pygccxml/pygccxml-648e8da-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pygccxml' +version = '648e8da' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pygccxml' +description = """Python package for easy C++ declarations navigation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +#github source: git clone https://github.com/gccxml/pygccxml.git 648e8da +sources = [SOURCE_TBZ2] + +dependencies = [ + ('Python', '3.5.1'), + ('CastXML', 'd5934bd'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-2c6c05b7a7d2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-2c6c05b7a7d2-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..9b9fa05275 --- /dev/null +++ b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-2c6c05b7a7d2-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pyplusplus' +version = '2c6c05b7a7d2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/ompl/pyplusplus' +description = """Py++ is a code generator for Boost.Python that simplifies + writing Python bindings of a C/C++ library + The tool is implemented as a Python module which is controlled by a user script.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/ompl/pyplusplus/get/'] +sources = ['%(version)s.zip'] + +dependencies = [ + ('Python', '3.5.1'), + ('pygccxml', '648e8da', '-Python-%(pyver)s'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-foss-2016a.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-foss-2016a.eb new file mode 100644 index 0000000000..c29bcc0a88 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6_makefile.patch b/easybuild/easyconfigs/t/Triangle/Triangle-1.6_makefile.patch new file mode 100644 index 0000000000..01806e267e --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6_makefile.patch @@ -0,0 +1,41 @@ +#Pick compiler and flags from environmental variables and make libtriangle.a from triangle.o +# Aug 04th 2016 by B. Hajgato (Free Univeristy Brussels - VUB) +--- makefile.orig 2005-07-28 02:22:01.000000000 +0200 ++++ makefile 2016-08-04 14:29:37.360139408 +0200 +@@ -18,7 +18,7 @@ + + # CC should be set to the name of your favorite C compiler. + +-CC = cc ++CC ?= cc + + # CSWITCHES is a list of all switches passed to the C compiler. I strongly + # recommend using the best level of optimization. I also strongly +@@ -73,7 +73,7 @@ + # + # CSWITCHES = -O -DNO_TIMER -DLINUX -I/usr/X11R6/include -L/usr/X11R6/lib + +-CSWITCHES = -O -DLINUX -I/usr/X11R6/include -L/usr/X11R6/lib ++CSWITCHES = $(CFLAGS) -DLINUX + + # TRILIBDEFS is a list of definitions used to compile an object code version + # of Triangle (triangle.o) to be called by another program. The file +@@ -96,7 +96,7 @@ + + all: $(BIN)triangle $(BIN)showme + +-trilibrary: $(BIN)triangle.o $(BIN)tricall ++trilibrary: $(BIN)libtriangle.a $(BIN)tricall + + $(BIN)triangle: $(SRC)triangle.c + $(CC) $(CSWITCHES) -o $(BIN)triangle $(SRC)triangle.c -lm +@@ -109,6 +109,9 @@ + $(CC) $(CSWITCHES) $(TRILIBDEFS) -c -o $(BIN)triangle.o \ + $(SRC)triangle.c + ++$(BIN)libtriangle.a: $(SRC)triangle.o ++ $(AR) cqs $(BIN)libtriangle.a triangle.o ++ + $(BIN)showme: $(SRC)showme.c + $(CC) $(CSWITCHES) -o $(BIN)showme $(SRC)showme.c -lX11 + -- GitLab From 0247df412e850641a9ba3722235493b7e85d3a02 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Aug 2016 12:28:09 +0200 Subject: [PATCH 113/701] SHLIB_EXT --- .../p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb index 6bf2fcfe65..a3b5ad77d1 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb @@ -41,8 +41,8 @@ dependencies = [ separate_build_dir = True configopts = '-DBOOST_ROOT=$EBROOTBOOST ' -configopts += '-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.so ' -configopts += '-DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.so ' +configopts += '-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT configopts += '-DCASTXML_EXECUTABLE=$EBROOTCASTXML/bin/castxml ' configopts += '-DPYGCCXML_PATH=$EBROOTPYGCCXML/lib/python%(pyshortver)s/site-packages/ ' configopts += '-DPYPLUSPLUS_PATH=$EBROOTPYPLUSPLUS/lib/python%(pyshortver)s/site-packages/ ' -- GitLab From f68c08a9883d7b26104e55ef6fd48d201bb2688d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Aug 2016 12:28:28 +0200 Subject: [PATCH 114/701] Add new binutils --- .../easyconfigs/b/binutils/binutils-2.27.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.27.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb new file mode 100644 index 0000000000..3309ac61a8 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb @@ -0,0 +1,19 @@ +name = 'binutils' +version = '2.27' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), +] + +moduleclass = 'tools' -- GitLab From 0f8d1dff64d5dc9f6ab1be06ffcc834c53fc0411 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Aug 2016 12:33:01 +0200 Subject: [PATCH 115/701] Added GCC/6.1.0 with binutils 2.27 --- easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb | 55 +++ .../GCC/mpfr-3.1.4-allpatches-20160804.patch | 453 ++++++++++++++++++ 2 files changed, 508 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb create mode 100644 easybuild/easyconfigs/g/GCC/mpfr-3.1.4-allpatches-20160804.patch diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb new file mode 100644 index 0000000000..bda699b863 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb @@ -0,0 +1,55 @@ +name = "GCC" +version = '6.1.0' + +binutilsver = '2.27' +versionsuffix = '-%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 = '3.1.4' + +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-6.1.1.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', binutilsver), +] + +patches = [('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '8fb6cb98b8459f5863328380fbf06bd1', # gcc-6.1.0.tar.bz2 + '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 + '13a670dca515e905856f95d13697fcdd', # mpfr-3.1.2-allpatches-20160522.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = False + +# 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-3.1.4-allpatches-20160804.patch b/easybuild/easyconfigs/g/GCC/mpfr-3.1.4-allpatches-20160804.patch new file mode 100644 index 0000000000..bcb2138fdf --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/mpfr-3.1.4-allpatches-20160804.patch @@ -0,0 +1,453 @@ +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-04-13 21:22:23.720604013 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-04-13 21:22:23.744603677 +0000 +@@ -0,0 +1 @@ ++unix-check +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-04-13 21:22:23.744603677 +0000 +@@ -1 +1 @@ +-3.1.4 ++3.1.4-p1 +diff -Naurd mpfr-3.1.4-a/src/mpfr-impl.h mpfr-3.1.4-b/src/mpfr-impl.h +--- mpfr-3.1.4-a/src/mpfr-impl.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr-impl.h 2016-04-13 21:22:23.736603789 +0000 +@@ -252,19 +252,6 @@ + # define MPFR_WIN_THREAD_SAFE_DLL 1 + #endif + +-/* Detect some possible inconsistencies under Unix. */ +-#if defined(__unix__) +-# if defined(_WIN32) +-# error "Both __unix__ and _WIN32 are defined" +-# endif +-# if __GMP_LIBGMP_DLL +-# error "__unix__ is defined and __GMP_LIBGMP_DLL is true" +-# endif +-# if defined(MPFR_WIN_THREAD_SAFE_DLL) +-# error "Both __unix__ and MPFR_WIN_THREAD_SAFE_DLL are defined" +-# endif +-#endif +- + #if defined(__MPFR_WITHIN_MPFR) || !defined(MPFR_WIN_THREAD_SAFE_DLL) + extern MPFR_THREAD_ATTR unsigned int __gmpfr_flags; + extern MPFR_THREAD_ATTR mpfr_exp_t __gmpfr_emin; +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4" ++#define MPFR_VERSION_STRING "3.1.4-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-04-13 21:22:23.744603677 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4"; ++ return "3.1.4-p1"; + } +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-05-22 19:59:43.838399677 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-05-22 19:59:43.866399168 +0000 +@@ -0,0 +1 @@ ++add-sub-ui-flags +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-05-22 19:59:43.866399168 +0000 +@@ -1 +1 @@ +-3.1.4-p1 ++3.1.4-p2 +diff -Naurd mpfr-3.1.4-a/src/add_ui.c mpfr-3.1.4-b/src/add_ui.c +--- mpfr-3.1.4-a/src/add_ui.c 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/add_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -49,6 +49,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_add(y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range(y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p1" ++#define MPFR_VERSION_STRING "3.1.4-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub_ui.c mpfr-3.1.4-b/src/sub_ui.c +--- mpfr-3.1.4-a/src/sub_ui.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -52,6 +52,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_sub (y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range (y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-05-22 19:59:43.866399168 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p1"; ++ return "3.1.4-p2"; + } +diff -Naurd mpfr-3.1.4-a/tests/tadd_ui.c mpfr-3.1.4-b/tests/tadd_ui.c +--- mpfr-3.1.4-a/tests/tadd_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tadd_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -69,7 +69,9 @@ + + /* nan + 2394875 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_add_ui (y, x, 2394875L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf + 2394875 == +inf */ +diff -Naurd mpfr-3.1.4-a/tests/tsub_ui.c mpfr-3.1.4-b/tests/tsub_ui.c +--- mpfr-3.1.4-a/tests/tsub_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -96,7 +96,9 @@ + + /* nan - 1 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_sub_ui (y, x, 1L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf - 1 == +inf */ +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-06-01 13:00:30.748711490 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-06-01 13:00:30.772711162 +0000 +@@ -0,0 +1 @@ ++sub1-overflow +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-06-01 13:00:30.772711162 +0000 +@@ -1 +1 @@ +-3.1.4-p2 ++3.1.4-p3 +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p2" ++#define MPFR_VERSION_STRING "3.1.4-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub1.c mpfr-3.1.4-b/src/sub1.c +--- mpfr-3.1.4-a/src/sub1.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub1.c 2016-06-01 13:00:30.760711326 +0000 +@@ -96,16 +96,15 @@ + /* A = S*ABS(B) +/- ulp(a) */ + MPFR_SET_EXP (a, MPFR_GET_EXP (b)); + MPFR_RNDRAW_EVEN (inexact, a, MPFR_MANT (b), MPFR_PREC (b), +- rnd_mode, MPFR_SIGN (a), +- if (MPFR_UNLIKELY ( ++MPFR_EXP (a) > __gmpfr_emax)) +- inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a))); +- /* inexact = mpfr_set4 (a, b, rnd_mode, MPFR_SIGN (a)); */ ++ rnd_mode, MPFR_SIGN (a), ++ MPFR_EXP (a)); + if (inexact == 0) + { + /* a = b (Exact) + But we know it isn't (Since we have to remove `c') + So if we round to Zero, we have to remove one ulp. + Otherwise the result is correctly rounded. */ ++ /* An overflow is not possible. */ ++ MPFR_ASSERTD (MPFR_EXP (a) <= __gmpfr_emax); + if (MPFR_IS_LIKE_RNDZ (rnd_mode, MPFR_IS_NEG (a))) + { + mpfr_nexttozero (a); +@@ -136,9 +135,14 @@ + i.e. inexact= MPFR_EVEN_INEX */ + if (MPFR_UNLIKELY (inexact == MPFR_EVEN_INEX*MPFR_INT_SIGN (a))) + { +- mpfr_nexttozero (a); ++ if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ mpfr_setmax (a, __gmpfr_emax); ++ else ++ mpfr_nexttozero (a); + inexact = -MPFR_INT_SIGN (a); + } ++ else if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a)); + MPFR_RET (inexact); + } + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-06-01 13:00:30.772711162 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p2"; ++ return "3.1.4-p3"; + } +diff -Naurd mpfr-3.1.4-a/tests/tsub.c mpfr-3.1.4-b/tests/tsub.c +--- mpfr-3.1.4-a/tests/tsub.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub.c 2016-06-01 13:00:30.760711326 +0000 +@@ -630,6 +630,135 @@ + } + } + ++static void ++check_max_almosteven (void) ++{ ++ mpfr_exp_t old_emin, old_emax; ++ mpfr_exp_t emin[2] = { MPFR_EMIN_MIN, -1000 }; ++ mpfr_exp_t emax[2] = { MPFR_EMAX_MAX, 1000 }; ++ int i; ++ ++ old_emin = mpfr_get_emin (); ++ old_emax = mpfr_get_emax (); ++ ++ for (i = 0; i < 2; i++) ++ { ++ mpfr_t a1, a2, b, c; ++ mpfr_prec_t p; ++ int neg, j, rnd; ++ ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ ++ p = MPFR_PREC_MIN + randlimb () % 70; ++ mpfr_init2 (a1, p); ++ mpfr_init2 (a2, p); ++ mpfr_init2 (b, p+1); ++ mpfr_init2 (c, MPFR_PREC_MIN); ++ ++ mpfr_setmax (b, 0); ++ mpfr_set_ui (c, 1, MPFR_RNDN); ++ ++ for (neg = 0; neg < 2; neg++) ++ { ++ for (j = 1; j >= 0; j--) ++ { ++ mpfr_set_exp (b, __gmpfr_emax - j); ++ RND_LOOP (rnd) ++ { ++ unsigned int flags1, flags2; ++ int inex1, inex2; ++ ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (rnd == MPFR_RNDN || MPFR_IS_LIKE_RNDZ (rnd, neg)) ++ { ++ inex1 = neg ? 1 : -1; ++ mpfr_setmax (a1, __gmpfr_emax - j); ++ } ++ else ++ { ++ inex1 = neg ? -1 : 1; ++ if (j == 0) ++ { ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ mpfr_set_inf (a1, 1); ++ } ++ else ++ { ++ mpfr_setmin (a1, __gmpfr_emax); ++ } ++ } ++ MPFR_SET_SIGN (a1, neg ? -1 : 1); ++ ++ mpfr_clear_flags (); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 1 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ ++ if (i == 0) ++ break; ++ ++ mpfr_clear_flags (); ++ set_emin (MPFR_EMIN_MIN); ++ set_emax (MPFR_EMAX_MAX); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ inex2 = mpfr_check_range (a2, inex2, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 2 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } /* j */ ++ ++ mpfr_neg (b, b, MPFR_RNDN); ++ mpfr_neg (c, c, MPFR_RNDN); ++ } /* neg */ ++ ++ mpfr_clears (a1, a2, b, c, (mpfr_ptr) 0); ++ } /* i */ ++ ++ set_emin (old_emin); ++ set_emax (old_emax); ++} ++ + #define TEST_FUNCTION test_sub + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -647,6 +776,7 @@ + check_rounding (); + check_diverse (); + check_inexact (); ++ check_max_almosteven (); + bug_ddefour (); + for (p=2; p<200; p++) + for (i=0; i<50; i++) +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-08-04 20:41:14.097592781 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-08-04 20:41:14.121592350 +0000 +@@ -0,0 +1 @@ ++c++11-compat +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-06-01 13:00:30.772711162 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-08-04 20:41:14.121592350 +0000 +@@ -1 +1 @@ +-3.1.4-p3 ++3.1.4-p4 +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-08-04 20:41:14.121592350 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p3" ++#define MPFR_VERSION_STRING "3.1.4-p4" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-06-01 13:00:30.772711162 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-08-04 20:41:14.121592350 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p3"; ++ return "3.1.4-p4"; + } +diff -Naurd mpfr-3.1.4-a/tests/tpow_z.c mpfr-3.1.4-b/tests/tpow_z.c +--- mpfr-3.1.4-a/tests/tpow_z.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tpow_z.c 2016-08-04 20:41:14.113592494 +0000 +@@ -26,7 +26,7 @@ + + #include "mpfr-test.h" + +-#define ERROR(str) do { printf("Error for "str"\n"); exit (1); } while (0) ++#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) + + static void + check_special (void) +diff -Naurd mpfr-3.1.4-a/tests/tset_si.c mpfr-3.1.4-b/tests/tset_si.c +--- mpfr-3.1.4-a/tests/tset_si.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tset_si.c 2016-08-04 20:41:14.113592494 +0000 +@@ -26,7 +26,7 @@ + + #include "mpfr-test.h" + +-#define ERROR(str) {printf("Error for "str"\n"); exit(1);} ++#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) + + static void + test_2exp (void) +diff -Naurd mpfr-3.1.4-a/tests/tset_sj.c mpfr-3.1.4-b/tests/tset_sj.c +--- mpfr-3.1.4-a/tests/tset_sj.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tset_sj.c 2016-08-04 20:41:14.113592494 +0000 +@@ -42,7 +42,7 @@ + + #else + +-#define ERROR(str) {printf("Error for "str"\n"); exit(1);} ++#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) + + static int + inexact_sign (int x) +diff -Naurd mpfr-3.1.4-a/tests/tsi_op.c mpfr-3.1.4-b/tests/tsi_op.c +--- mpfr-3.1.4-a/tests/tsi_op.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsi_op.c 2016-08-04 20:41:14.113592494 +0000 +@@ -26,14 +26,16 @@ + + #include "mpfr-test.h" + +-#define ERROR1(s, i, z, exp) \ +-{\ +- printf("Error for "s" and i=%d\n", i);\ +- printf("Expected %s\n", exp);\ +- printf("Got "); mpfr_out_str (stdout, 16, 0, z, MPFR_RNDN);\ +- putchar ('\n');\ +- exit(1);\ +-} ++#define ERROR1(s,i,z,exp) \ ++ do \ ++ { \ ++ printf ("Error for " s " and i=%d\n", i); \ ++ printf ("Expected %s\n", exp); \ ++ printf ("Got "); mpfr_out_str (stdout, 16, 0, z, MPFR_RNDN); \ ++ putchar ('\n'); \ ++ exit(1); \ ++ } \ ++ while (0) + + const struct { + const char * op1; -- GitLab From e738c3a262bf74ddf74435d0a6336385f2a7baa7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Aug 2016 16:09:43 +0200 Subject: [PATCH 116/701] Create GCCcore 6.1 and GCC on top of that --- .../b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb | 27 ++++++++++ .../b/binutils/binutils-2.27-GCCcore-6.1.0.eb | 21 ++++++++ .../f/flex/flex-2.6.0-GCCcore-6.1.0.eb | 21 ++++++++ easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb | 50 ++++------------- .../easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 54 +++++++++++++++++++ .../mpfr-3.1.4-allpatches-20160804.patch | 0 .../m/M4/M4-1.4.17-GCCcore-6.1.0.eb | 26 +++++++++ .../z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb | 25 +++++++++ 8 files changed, 184 insertions(+), 40 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb rename easybuild/easyconfigs/g/{GCC => GCCcore}/mpfr-3.1.4-allpatches-20160804.patch (100%) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..85a3abd7ad --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +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': 'GCCcore', 'version': '6.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..4c7f93641a --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.27' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.1.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # 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) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..687cf19d5f --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -0,0 +1,21 @@ +name = 'flex' +version = '2.6.0' + +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': 'GCCcore', 'version': '6.1.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +parallel = 1 + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb index bda699b863..4faa0a48e8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb @@ -1,4 +1,6 @@ -name = "GCC" +easyblock = 'Bundle' + +name = 'GCC' version = '6.1.0' binutilsver = '2.27' @@ -10,46 +12,14 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': ''} -mpfr_version = '3.1.4' - -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-6.1.1.tar.bz2', - 'mpfr-%s.tar.bz2' % mpfr_version, - 'mpc-1.0.3.tar.gz', - 'isl-0.16.1.tar.bz2', -] - -builddependencies = [ - ('M4', '1.4.17'), - ('binutils', binutilsver), +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), ] -patches = [('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] - -checksums = [ - '8fb6cb98b8459f5863328380fbf06bd1', # gcc-6.1.0.tar.bz2 - '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 - 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.tar.gz - 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 - '13a670dca515e905856f95d13697fcdd', # mpfr-3.1.2-allpatches-20160522.patch -] - -languages = ['c', 'c++', 'fortran'] - -withisl = False - -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 +altroot = 'GCCcore' +altversion = 'GCCcore' +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb new file mode 100644 index 0000000000..d3bf1f3973 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '6.1.0' + +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': ''} + +mpfr_version = '3.1.4' + +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 = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.1.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.27'), +] + +patches = [('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '8fb6cb98b8459f5863328380fbf06bd1', # gcc-6.1.0.tar.bz2 + '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 + '13a670dca515e905856f95d13697fcdd', # mpfr-3.1.2-allpatches-20160522.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = False + +# 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-3.1.4-allpatches-20160804.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160804.patch similarity index 100% rename from easybuild/easyconfigs/g/GCC/mpfr-3.1.4-allpatches-20160804.patch rename to easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160804.patch diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..2bc1e5e46b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb @@ -0,0 +1,26 @@ +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': 'GCCcore', 'version': '6.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..47a40a4035 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb @@ -0,0 +1,25 @@ +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': 'GCCcore', 'version': '6.1.0'} +toolchainopts = {'pic': True} + +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', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 85cace9a432ac020376e6d01b58701bdb66e14f6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Aug 2016 16:19:00 +0200 Subject: [PATCH 117/701] Fix checksum --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index d3bf1f3973..83a80912f2 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -37,7 +37,7 @@ patches = [('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % m checksums = [ '8fb6cb98b8459f5863328380fbf06bd1', # gcc-6.1.0.tar.bz2 - '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + '4c175f86e11eb32d8bf9872ca3a8e11d', # gmp-6.1.1.tar.bz2 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.tar.gz 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 -- GitLab From 02a9e0198dc5e3ec0bdbd22ca8e033736cbe63a5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Aug 2016 16:31:17 +0200 Subject: [PATCH 118/701] Newest CMake 3.6.1 --- .../c/CMake/CMake-3.6.1-foss-2016b.eb | 31 +++++++++++++++++++ .../c/CMake/CMake-3.6.1-intel-2016b.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb new file mode 100644 index 0000000000..c1386c78f8 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +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': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # 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', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb new file mode 100644 index 0000000000..425f4e01e2 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +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': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # 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', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 351db98bd156c2961efd6228a8e9e0975ab7d9ef Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Aug 2016 16:33:27 +0200 Subject: [PATCH 119/701] Added LLVM 3.8.1 --- .../l/LLVM/LLVM-3.8.1-foss-2016b.eb | 42 +++++++++++++++++++ .../l/LLVM/LLVM-3.8.1-intel-2016b.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-foss-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-foss-2016b.eb new file mode 100644 index 0000000000..9591135989 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-foss-2016b.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.1' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb new file mode 100644 index 0000000000..c220e06399 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.1' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From 192f714e4b394cc9e83347e1d45811d8e4fb7c49 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Aug 2016 17:31:41 +0200 Subject: [PATCH 120/701] Add Python/2.7.12 bare --- .../a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb | 26 ++++++++++++ .../a/Automake/Automake-1.15-GCCcore-5.4.0.eb | 33 +++++++++++++++ .../Autotools-20150215-GCCcore-5.4.0.eb | 17 ++++++++ .../b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb | 15 +++++++ .../g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb | 30 ++++++++++++++ .../l/libffi/libffi-3.2.1-GCC-5.4.0-2.26.eb | 23 +++++++++++ .../libreadline-6.3-GCCcore-5.4.0.eb | 32 +++++++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb | 17 ++++++++ .../n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb | 38 ++++++++++++++++++ .../Python-2.7.12-GCC-5.4.0-2.26-bare.eb | 31 ++++++++++++++ .../s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb | 40 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb | 25 ++++++++++++ .../t/Tk/Tk-8.6.5-GCC-5.4.0-2.26.eb | 26 ++++++++++++ .../z/zlib/zlib-1.2.8-GCC-5.4.0-2.26.eb | 22 ++++++++++ 14 files changed, 375 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..2c747cb3eb --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.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': 'GCCcore', 'version': '5.4.0'} + +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-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..834421055b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.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': 'GCCcore', 'version': '5.4.0'} + +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-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..b7e948c549 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.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': 'GCCcore', 'version': '5.4.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..42b488a1d6 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..9c102d359e --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.1' + +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': '5.4.0-2.26'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215', '', ('GCCcore', '5.4.0')), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..54836f2681 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} + +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' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..aef1e3baa8 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb @@ -0,0 +1,32 @@ +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': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +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/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..a9916c30e6 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.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': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..afda72a745 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +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': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +builddependencies = [('binutils', '2.26')] + +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", "ncurses%(version_major)s-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.%s' % (x, y, SHLIB_EXT) 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/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb new file mode 100644 index 0000000000..d181065925 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.12' +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': 'GCC', 'version': '5.4.0-2.26'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3', '', ('GCCcore', '5.4.0')), + ('ncurses', '6.0', '', ('GCCcore', '5.4.0')), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), + ('GMP', '6.1.1'), + ('libffi', '3.2.1'), + # 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', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..1edf413323 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.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 = '3.13.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = ['http://www.sqlite.org/2016/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3', '', ('GCCcore', '5.4.0')), + ('Tcl', '8.6.5'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..cee27f6687 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.5' + +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': '5.4.0-2.26'} + +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-8.6.5-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..f2a063069a --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCC-5.4.0-2.26.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +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': '5.4.0-2.26'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..2155a965c0 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.4.0-2.26.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': '5.4.0-2.26'} +toolchainopts = {'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 7f61c49897d3badbc24ffe4166e30febe23f88f6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Aug 2016 17:32:30 +0200 Subject: [PATCH 121/701] Add Clang 3.8.1 --- .../c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb | 31 ++++++++++++ .../c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb | 50 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..6a2229239d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +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': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # 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', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..0a480eaace --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.8.1" + +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': '5.4.0-2.26'} +# 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", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.1'), +# ('ISL', '0.17.1'), +] + +builddependencies = [ + ('CMake', '3.6.1', '', ('GCCcore', '5.4.0')), + ('Python', '2.7.12', '-bare'), + ('libxml2', '2.9.4'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' -- GitLab From 2cd607ff8ad3287ae910bfb5830e217b205dc9ba Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Aug 2016 17:38:50 +0200 Subject: [PATCH 122/701] Forgot libxml2 easyconfig --- .../l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..980c2fea95 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.4' + +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': '5.4.0-2.26'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' -- GitLab From 655be03d33309c2646c1f859f51c4a6255fcf3f9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 9 Aug 2016 10:58:19 +0200 Subject: [PATCH 123/701] Add binutils as build dep for GCCcore easyconfigs --- easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb | 2 ++ .../easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb | 2 ++ easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb index 6a2229239d..874d63a543 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb @@ -21,6 +21,8 @@ dependencies = [ #('OpenSSL', '1.0.1s'), ] +builddependencies = [('binutils', '2.27')] + osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb index aef1e3baa8..b756c22ee2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb @@ -19,6 +19,8 @@ patches = ['libreadline-%(version)s-bugfix.patch'] dependencies = [('ncurses', '6.0')] +builddependencies = [('binutils', '2.27')] + # for the termcap symbols, use EB ncurses preconfigopts = "env LDFLAGS='-lncurses'" diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb index a9916c30e6..5cf762ffe7 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -14,4 +14,6 @@ source_urls = [GNU_SOURCE] dependencies = [('M4', '1.4.17')] +builddependencies = [('binutils', '2.27')] + moduleclass = 'lib' -- GitLab From 5ef6d6e06a6fd60b3b755b2abdbd596632fcec81 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 9 Aug 2016 11:00:26 +0200 Subject: [PATCH 124/701] Use dummy binutils! --- easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb index 874d63a543..cc331f51e0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb @@ -21,7 +21,7 @@ dependencies = [ #('OpenSSL', '1.0.1s'), ] -builddependencies = [('binutils', '2.27')] +builddependencies = [('binutils', '2.27', '', True)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb index b756c22ee2..4069dd92de 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ patches = ['libreadline-%(version)s-bugfix.patch'] dependencies = [('ncurses', '6.0')] -builddependencies = [('binutils', '2.27')] +builddependencies = [('binutils', '2.27', '', True)] # for the termcap symbols, use EB ncurses preconfigopts = "env LDFLAGS='-lncurses'" diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb index 5cf762ffe7..6e5b5ddd96 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -14,6 +14,6 @@ source_urls = [GNU_SOURCE] dependencies = [('M4', '1.4.17')] -builddependencies = [('binutils', '2.27')] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lib' -- GitLab From cb0011296425b8c7e9729af65d98b96842ee5f0b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 9 Aug 2016 11:35:05 +0200 Subject: [PATCH 125/701] Use correct version of binutils --- easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb index cc331f51e0..b63b93d99d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb @@ -21,7 +21,7 @@ dependencies = [ #('OpenSSL', '1.0.1s'), ] -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.26', '', True)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb index 4069dd92de..1bd3a7527a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ patches = ['libreadline-%(version)s-bugfix.patch'] dependencies = [('ncurses', '6.0')] -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.26', '', True)] # for the termcap symbols, use EB ncurses preconfigopts = "env LDFLAGS='-lncurses'" diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb index 6e5b5ddd96..de49f67f93 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -14,6 +14,6 @@ source_urls = [GNU_SOURCE] dependencies = [('M4', '1.4.17')] -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.26', '', True)] moduleclass = 'lib' -- GitLab From db492748b1cece7d6c3180ea303edb74f5e48a3f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 10 Aug 2016 11:58:41 +0200 Subject: [PATCH 126/701] Use older CMake for LLVM/3.8.1 with intel/2016b --- easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb index c220e06399..243e52187d 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb @@ -19,7 +19,7 @@ source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ - ('CMake', '3.6.1'), + ('CMake', '3.5.2'), ('Python', '2.7.12'), ] -- GitLab From 05ae076a8bff75e40639e566f00a3f25237921d3 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 10 Aug 2016 11:59:06 +0200 Subject: [PATCH 127/701] Currently, CMake/3.6.1 doesn't build with intel/2016b Removing util fix is found. --- .../c/CMake/CMake-3.6.1-intel-2016b.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb deleted file mode 100644 index 425f4e01e2..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.6.1' - -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': '2016b'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = '-- -DCMAKE_USE_OPENSSL=1' - -dependencies = [ - ('ncurses', '6.0'), - # 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', '1.0.1s'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' -- GitLab From 3c982c97741992df6b1cab5aaf38bc2f0b12db20 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 10 Aug 2016 21:16:47 -0500 Subject: [PATCH 128/701] Adding an Easyconfig for SOLAR-Eclipse v8.1.1 --- .../s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb diff --git a/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb b/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb new file mode 100644 index 0000000000..7eccd82679 --- /dev/null +++ b/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'SOLAR-Eclipse' +version = '8.1.1' + +homepage = 'http://solar-eclipse-genetics.org/' +description = """SOLAR-Eclipse is an extensive, flexible +software package for genetic variance components analysis, +including linkage analysis, quantitative genetic analysis, +SNP association analysis (QTN and QTLD), and covariate screening. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://www.nitrc.org/frs/download.php/8542/'] +sources = ['solar_linux.tar.gz'] + +checksums = ['cbc05fb6c39853a888d9ee151a383461'] + +postinstallcmds = ["./install_solar %(installdir)s %(installdir)s", + "./install_rlwrap %(installdir)s"] + +modextravars = {'SOLAR_BIN': '%(installdir)s/bin', + 'SOLAR_LIB': '%(installdir)s/lib'} +sanity_check_paths = { + 'files': ["bin/solarmain", "bin/rlwrap"], + 'dirs': ["lib", ] +} + +moduleclass = 'bio' + -- GitLab From 18ad942a312995458ccd2b0a97bac21e389e0699 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 16 Aug 2016 15:13:17 +0800 Subject: [PATCH 129/701] fix style and comments --- .../VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 22 ++++++++++++------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 29745c333e..92a0ece294 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -14,20 +14,26 @@ toolchainopts = {'usempi': True} # Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code sources = [SOURCELOWER_TAR_GZ] -patches = ['patch.5.4.1.08072015', 'patch.5.4.1.27082015', 'patch.5.4.1.06112015'] - -checksums = ['57c2b07d0f70987000033984e913f1a6', # vasp.5.4.1.tar.gz - 'ee242452bba6bb37459745f4617649d7', # patch.5.4.1.08072015 - 'b137eb13804a60df382e77495dc738f9', # patch.5.4.1.27082015 - 'd64b8f0ae861db7a76e6e9c9ffa188a1', # patch.5.4.1.06112015 - ] +# patches from http://cms.mpi.univie.ac.at/wiki/index.php/Installing_VASP +patches = [ + 'vasp.5.4.1.08072015.patch', + 'vasp.5.4.1.27082015.patch', + 'vasp.5.4.1.06112015.patch', +] + +checksums = [ + '57c2b07d0f70987000033984e913f1a6', # vasp.5.4.1.tar.gz + 'ee242452bba6bb37459745f4617649d7', # vasp.5.4.1.08072015.patch + 'b137eb13804a60df382e77495dc738f9', # vasp.5.4.1.27082015.patch + 'd64b8f0ae861db7a76e6e9c9ffa188a1', # vasp.5.4.1.06112015.patch +] prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' # path to libfftw3xf_intel.a is hardcoded in makefile.include prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$(FFTW_LIB_DIR)|" makefile.include && ' -# we use static mkl later +# remove mkl flag to prevent mixing dynamic libs with the static libs in LIBBLACS/SCALAPACK prebuildopts += 'sed -i "s|-mkl||" makefile.include && ' # VASP uses LIBS as a list of folders -- GitLab From 2ec51b34b20195147bf353dfa6fc277d239e1305 Mon Sep 17 00:00:00 2001 From: Liang Date: Wed, 17 Aug 2016 16:02:02 +0200 Subject: [PATCH 130/701] foss 2016b with hybrid parallelism for QE, patch file attached --- .../QuantumESPRESSO/QE_gfortran_f90rule.patch | 12 ++++ ...QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 57 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QE_gfortran_f90rule.patch create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QE_gfortran_f90rule.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QE_gfortran_f90rule.patch new file mode 100644 index 0000000000..85d62f606b --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QE_gfortran_f90rule.patch @@ -0,0 +1,12 @@ +diff -rupN espresso-5.4.0.orig/install/make.sys.in espresso-5.4.0/install/make.sys.in +--- espresso-5.4.0.orig/install/make.sys.in 2016-04-24 23:19:25.000000000 +0200 ++++ espresso-5.4.0/install/make.sys.in 2016-06-11 15:08:15.869499000 +0200 +@@ -13,7 +13,7 @@ + # remember the tabulator in the first column !!! + + .f90.o: +- @f90rule@ ++ $(MPIF90) $(F90FLAGS) -c $< + + # .f.o and .c.o: do not modify + diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb new file mode 100644 index 0000000000..7a2801e626 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -0,0 +1,57 @@ +name = 'QuantumESPRESSO' +version = '5.4.0' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True, 'openmp': True} + +# this list was determined from QE 5.4.0 version release +sources = [ + # Common source + 'espresso-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + # Other sources + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.tar.gz', + 'pwcond-%(version)s.tar.gz', + 'xspectra-%(version)s.tar.gz' , + 'PWgui-%(version)s.tar.gz' , + 'EPW-%(version)s.tar.gz' , + 'test-suite-%(version)s.tar.gz' , + 'GWW-%(version)s.tar.gz' , +] +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # Almost all + 'http://www.qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz + # These will not be used because of the 404 signal not found from the previous link. + 'http://www.qe-forge.org/gf/download/frsrelease/211/961/', # PWgui-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/954/', # atomic-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/959/', # neb-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/962/', # PHonon-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/960/', # pwcond-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/958/', # xspectra-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/969/', # EPW-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/963/', # test-suite-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/957/', # GWW-5.4.0.tar.gz +] + +# Hybrid option exist only for backward compatibility, use toolchain option openmp instead. +# hybrid = True +# Patch file to avoil the CPP problem generated by different OSes +patches = ['QE_gfortran_f90rule.patch'] + +# packages included in 5.4.0 version of QE. Met errors when try to include gipaw, yambo and someother packages. +buildopts = 'all tddfpt neb xspectra ph ' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' + -- GitLab From 24a389eb0c10d7b7a7075facdbdefb7d3b14f33c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 17 Aug 2016 16:25:17 +0200 Subject: [PATCH 131/701] Fix remarks --- ...4.0.eb => Autoconf-2.69-GCC-5.4.0-2.26.eb} | 2 +- ...4.0.eb => Automake-1.15-GCC-5.4.0-2.26.eb} | 2 +- ...b => Autotools-20150215-GCC-5.4.0-2.26.eb} | 2 +- ...5.4.0.eb => CMake-3.6.1-GCC-5.4.0-2.26.eb} | 4 +-- .../c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb | 3 +-- .../g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb | 2 +- ...0.eb => libreadline-6.3-GCC-5.4.0-2.26.eb} | 4 +-- ...4.0.eb => libtool-2.4.6-GCC-5.4.0-2.26.eb} | 2 +- .../m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb | 26 +++++++++++++++++++ ...5.4.0.eb => ncurses-6.0-GCC-5.4.0-2.26.eb} | 4 +-- .../Python-2.7.12-GCC-5.4.0-2.26-bare.eb | 4 +-- .../s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb | 2 +- 12 files changed, 38 insertions(+), 19 deletions(-) rename easybuild/easyconfigs/a/Autoconf/{Autoconf-2.69-GCCcore-5.4.0.eb => Autoconf-2.69-GCC-5.4.0-2.26.eb} (94%) rename easybuild/easyconfigs/a/Automake/{Automake-1.15-GCCcore-5.4.0.eb => Automake-1.15-GCC-5.4.0-2.26.eb} (93%) rename easybuild/easyconfigs/a/Autotools/{Autotools-20150215-GCCcore-5.4.0.eb => Autotools-20150215-GCC-5.4.0-2.26.eb} (88%) rename easybuild/easyconfigs/c/CMake/{CMake-3.6.1-GCCcore-5.4.0.eb => CMake-3.6.1-GCC-5.4.0-2.26.eb} (88%) rename easybuild/easyconfigs/l/libreadline/{libreadline-6.3-GCCcore-5.4.0.eb => libreadline-6.3-GCC-5.4.0-2.26.eb} (91%) rename easybuild/easyconfigs/l/libtool/{libtool-2.4.6-GCCcore-5.4.0.eb => libtool-2.4.6-GCC-5.4.0-2.26.eb} (89%) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb rename easybuild/easyconfigs/n/ncurses/{ncurses-6.0-GCCcore-5.4.0.eb => ncurses-6.0-GCC-5.4.0-2.26.eb} (93%) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-5.4.0-2.26.eb similarity index 94% rename from easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb rename to easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-5.4.0-2.26.eb index 2c747cb3eb..a3fab7ed38 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-5.4.0-2.26.eb @@ -10,7 +10,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she 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': 'GCCcore', 'version': '5.4.0'} +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb similarity index 93% rename from easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb rename to easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb index 834421055b..e42ff28556 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb @@ -18,7 +18,7 @@ version = "1.15" homepage = 'http://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" -toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-5.4.0-2.26.eb similarity index 88% rename from easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb rename to easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-5.4.0-2.26.eb index b7e948c549..1452a8b0ad 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ 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': 'GCCcore', 'version': '5.4.0'} +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} dependencies = [ ('Autoconf', '2.69'), # 20120424 diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb similarity index 88% rename from easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb rename to easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb index b63b93d99d..97b2282312 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb @@ -7,7 +7,7 @@ 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': 'GCCcore', 'version': '5.4.0'} +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] @@ -21,8 +21,6 @@ dependencies = [ #('OpenSSL', '1.0.1s'), ] -builddependencies = [('binutils', '2.26', '', True)] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb index 0a480eaace..3c6cb72c88 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb @@ -32,11 +32,10 @@ sources = [ dependencies = [ ('GMP', '6.1.1'), -# ('ISL', '0.17.1'), ] builddependencies = [ - ('CMake', '3.6.1', '', ('GCCcore', '5.4.0')), + ('CMake', '3.6.1'), ('Python', '2.7.12', '-bare'), ('libxml2', '2.9.4'), ] diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb index 9c102d359e..e326069638 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] builddependencies = [ - ('Autotools', '20150215', '', ('GCCcore', '5.4.0')), + ('Autotools', '20150215'), ] # enable C++ interface diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-5.4.0-2.26.eb similarity index 91% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb rename to easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-5.4.0-2.26.eb index 1bd3a7527a..645b3114fd 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-5.4.0-2.26.eb @@ -9,7 +9,7 @@ description = """The GNU Readline library provides a set of functions for use by 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': 'GCCcore', 'version': '5.4.0'} +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] @@ -19,8 +19,6 @@ patches = ['libreadline-%(version)s-bugfix.patch'] dependencies = [('ncurses', '6.0')] -builddependencies = [('binutils', '2.26', '', True)] - # for the termcap symbols, use EB ncurses preconfigopts = "env LDFLAGS='-lncurses'" diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb similarity index 89% rename from easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb rename to easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb index de49f67f93..b7b866f5e7 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb @@ -7,7 +7,7 @@ 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': 'GCCcore', 'version': '5.4.0'} +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..1dd87ec971 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb @@ -0,0 +1,26 @@ +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': 'GCC', 'version': '5.4.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-5.4.0-2.26.eb similarity index 93% rename from easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb rename to easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-5.4.0-2.26.eb index afda72a745..a13213588d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-5.4.0-2.26.eb @@ -8,7 +8,7 @@ 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.""" -toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] @@ -16,8 +16,6 @@ sources = [SOURCE_TAR_GZ] patches = ['ncurses-%(version)s_gcc-5.patch'] -builddependencies = [('binutils', '2.26')] - configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb index d181065925..fb337a3d58 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb @@ -15,8 +15,8 @@ sources = [SOURCE_TGZ] dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), - ('libreadline', '6.3', '', ('GCCcore', '5.4.0')), - ('ncurses', '6.0', '', ('GCCcore', '5.4.0')), + ('libreadline', '6.3'), + ('ncurses', '6.0'), ('SQLite', '3.13.0'), ('Tk', '8.6.5'), ('GMP', '6.1.1'), diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb index 1edf413323..c8632b48d5 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb @@ -27,7 +27,7 @@ version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_min sources = ['sqlite-autoconf-%s.tar.gz' % version_str] dependencies = [ - ('libreadline', '6.3', '', ('GCCcore', '5.4.0')), + ('libreadline', '6.3'), ('Tcl', '8.6.5'), ] -- GitLab From 1751276f550e84ddf8ab794598a55747309528de Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 17 Aug 2016 16:50:55 +0200 Subject: [PATCH 132/701] Fix conflicts --- .../easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb | 2 -- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb | 3 --- 2 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb index b7b866f5e7..ba5556d8b5 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb @@ -14,6 +14,4 @@ source_urls = [GNU_SOURCE] dependencies = [('M4', '1.4.17')] -builddependencies = [('binutils', '2.26', '', True)] - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb index 1dd87ec971..747a5dbe94 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb @@ -13,9 +13,6 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] - configopts = "--enable-cxx" sanity_check_paths = { -- GitLab From dbd9e8819a03aef8721767d2fde726ac57d9063e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 17 Aug 2016 22:18:43 +0200 Subject: [PATCH 133/701] modluafooter and commant for modxxxfooter added --- .../Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb index 9267180d04..93d2f1fa5c 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb @@ -45,6 +45,10 @@ sanity_check_paths = { 'dirs': [] } +# Yambo is installed with QuantumESPRESSO. I do not like if the same program (with different versions) +# is twice in the PATH. Withouth removing the QuantumESPRESSO one, this version of Yambo would be used, +# because it is earlier in the PATH modtclfooter = "remove-path PATH $::env(EBROOTQUANTUMESPRESSO)/espresso-%s/YAMBO/bin" % qever +modluafooter = 'remove_path("PATH", os.getenv(EBROOTQUANTUMESPRESSO) .. "/espresso-%s/YAMBO/bin")' % qever moduleclass = 'phys' -- GitLab From 8e02814f157a3b7e1a28dc896e35c73ac567e8e5 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 17 Aug 2016 20:08:24 -0500 Subject: [PATCH 134/701] Adding Easyconfig for S.A.G.E. --- .../easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb diff --git a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb b/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb new file mode 100644 index 0000000000..28ef2c7ef6 --- /dev/null +++ b/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'S.A.G.E.' +version = '6.3' + +homepage = 'https://code.google.com/archive/p/opensage/' +description = """ S.A.G.E. (Statistical Analysis for Genetic +Epidemiology) is free software package containing programs for +use in the genetic analysis of family, pedigree and individual data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/opensage/'] +sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] + +sanity_check_paths = { + 'files': ["bin/freq", "bin/ageon", "bin/segreg"], + 'dirs': ["data_files", "documentaion"] +} + +moduleclass = 'bio' -- GitLab From 47fca3ba858aac95847983a31fa5a01213e0a6af Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 17 Aug 2016 20:10:00 -0500 Subject: [PATCH 135/701] Removing SOLAR-Eclipse from this PR --- .../s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb diff --git a/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb b/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb deleted file mode 100644 index 7eccd82679..0000000000 --- a/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Ravi Tripathi -# Email: ravi89@uab.edu - -easyblock = "Tarball" - -name = 'SOLAR-Eclipse' -version = '8.1.1' - -homepage = 'http://solar-eclipse-genetics.org/' -description = """SOLAR-Eclipse is an extensive, flexible -software package for genetic variance components analysis, -including linkage analysis, quantitative genetic analysis, -SNP association analysis (QTN and QTLD), and covariate screening. """ - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['https://www.nitrc.org/frs/download.php/8542/'] -sources = ['solar_linux.tar.gz'] - -checksums = ['cbc05fb6c39853a888d9ee151a383461'] - -postinstallcmds = ["./install_solar %(installdir)s %(installdir)s", - "./install_rlwrap %(installdir)s"] - -modextravars = {'SOLAR_BIN': '%(installdir)s/bin', - 'SOLAR_LIB': '%(installdir)s/lib'} -sanity_check_paths = { - 'files': ["bin/solarmain", "bin/rlwrap"], - 'dirs': ["lib", ] -} - -moduleclass = 'bio' - -- GitLab From 10898d1b53734b19ea73c8617fa3bf051250eb6c Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 17 Aug 2016 20:33:40 -0500 Subject: [PATCH 136/701] Adding Easyconfig for Maq --- easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb | 28 ++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb diff --git a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb new file mode 100644 index 0000000000..e769a35218 --- /dev/null +++ b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'Maq' +version = '0.7.0' + +homepage = 'http://maq.sourceforge.net/maq-man.shtml' +description = """ Maq is a software that builds mapping +assemblies from short reads generated by the +next-generation sequencing machines. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://sourceforge.net/projects/maq/files/maq/0.7.0/'] +sources = ['maq-%(version)s_x86_64-linux.tar.bz2'] + +modextrapaths = {'PATH': ''} + +checksums= ["65edff1529c84783d0a4b9208a91efa9"] +sanity_check_paths = { + 'files': ["asub", "maq", "maq.pdf", "maq.1", "solid2fastq.pl"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 3e26626072e02f020213b05ffc40035117415003 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 17 Aug 2016 20:35:06 -0500 Subject: [PATCH 137/701] Removing SOLAR-Eclipse from this PR --- .../s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb diff --git a/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb b/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb deleted file mode 100644 index 7eccd82679..0000000000 --- a/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Ravi Tripathi -# Email: ravi89@uab.edu - -easyblock = "Tarball" - -name = 'SOLAR-Eclipse' -version = '8.1.1' - -homepage = 'http://solar-eclipse-genetics.org/' -description = """SOLAR-Eclipse is an extensive, flexible -software package for genetic variance components analysis, -including linkage analysis, quantitative genetic analysis, -SNP association analysis (QTN and QTLD), and covariate screening. """ - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['https://www.nitrc.org/frs/download.php/8542/'] -sources = ['solar_linux.tar.gz'] - -checksums = ['cbc05fb6c39853a888d9ee151a383461'] - -postinstallcmds = ["./install_solar %(installdir)s %(installdir)s", - "./install_rlwrap %(installdir)s"] - -modextravars = {'SOLAR_BIN': '%(installdir)s/bin', - 'SOLAR_LIB': '%(installdir)s/lib'} -sanity_check_paths = { - 'files': ["bin/solarmain", "bin/rlwrap"], - 'dirs': ["lib", ] -} - -moduleclass = 'bio' - -- GitLab From cbfd201bc36d524a06dec3645d4729a4996ca798 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Wed, 17 Aug 2016 22:51:20 -0500 Subject: [PATCH 138/701] Adding easyconfig for ASHS --- .../a/ASHS/ASHS-rev103_20140612.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb diff --git a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb new file mode 100644 index 0000000000..0075d9362a --- /dev/null +++ b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'ASHS' +version = 'rev103_20140612' + +homepage = 'https://sites.google.com/site/hipposubfields/home' +description = """ Automatic Segmentation of Hippocampal Subfields (ASHS) """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +#You need to create an account to download the source +#from https://www.nitrc.org/frs/?group_id=370 +sources = ['ashs_Linux64_%(version)s.tgz'] + +modextravars = {'ASHS_ROOT': '%(installdir)s'} + +checksums= ["07fea2883b856af8797b200212b72e71"] + +sanity_check_paths = { + 'files': ["bin/ashs_main.sh", "bin/ashs_template_qsub.sh", "bin/ashs_train.sh", + "bin/ashs_util_makepdf.sh"], + 'dirs': ["ext"] +} + +moduleclass = 'bio' -- GitLab From 37dbf2252cbeb40be861bf0e48f2395e18e4c378 Mon Sep 17 00:00:00 2001 From: Liang Date: Thu, 18 Aug 2016 10:43:32 +0200 Subject: [PATCH 139/701] Update comments in .eb file --- .../QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index 7a2801e626..7a77f720dd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -42,12 +42,12 @@ source_urls = [ 'http://www.qe-forge.org/gf/download/frsrelease/211/957/', # GWW-5.4.0.tar.gz ] -# Hybrid option exist only for backward compatibility, use toolchain option openmp instead. +# Hybrid option exists only for backward compatibility, use toolchain option openmp instead. # hybrid = True -# Patch file to avoil the CPP problem generated by different OSes +# Patch file to avoid the CPP problem generated by different OSes patches = ['QE_gfortran_f90rule.patch'] -# packages included in 5.4.0 version of QE. Met errors when try to include gipaw, yambo and someother packages. +# packages included in 5.4.0 version of QE. We met errors when try to include gipaw, yambo and someother packages. buildopts = 'all tddfpt neb xspectra ph ' # parallel build tends to fail -- GitLab From ec01a36aa14e09a70d275371b746ad18f8a511ac Mon Sep 17 00:00:00 2001 From: Liang Date: Thu, 18 Aug 2016 15:59:55 +0200 Subject: [PATCH 140/701] Uncomment hybrid= True in .eb file --- .../QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index 7a77f720dd..a9d7deba0f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -43,7 +43,7 @@ source_urls = [ ] # Hybrid option exists only for backward compatibility, use toolchain option openmp instead. -# hybrid = True +hybrid = True # Patch file to avoid the CPP problem generated by different OSes patches = ['QE_gfortran_f90rule.patch'] -- GitLab From 9fe84ee517c034ef2e14710c7dd243fb7c20a1fa Mon Sep 17 00:00:00 2001 From: Liang Date: Thu, 18 Aug 2016 16:47:20 +0200 Subject: [PATCH 141/701] Add versionsuffix= '-hybrid' .eb file --- .../q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index a9d7deba0f..9c0424411c 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -1,5 +1,6 @@ name = 'QuantumESPRESSO' version = '5.4.0' +versionsuffix = '-hybrid' homepage = 'http://www.pwscf.org/' description = """Quantum ESPRESSO is an integrated suite of computer codes -- GitLab From 6cf0f35d0900f098951261b912147cab25e09f69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Aug 2016 12:37:21 +0200 Subject: [PATCH 142/701] add easyconfig Boost-1.61.0-intel-2016b-Python-2.7.12.eb --- .../Boost-1.61.0-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..015aad2716 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.61.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From d0ab24cb67bca60eb488d53fa0c9f6ebe6f825dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Aug 2016 12:42:56 +0200 Subject: [PATCH 143/701] add easyconfig MPFR-3.1.4-intel-2016b.eb --- .../m/MPFR/MPFR-3.1.4-intel-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016b.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016b.eb new file mode 100644 index 0000000000..1d9a8972b9 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.1')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 8555745033be6a90275ea74c032f9acf9370e4a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Aug 2016 14:19:11 +0200 Subject: [PATCH 144/701] add easyconfig minieigen-0.5.3-intel-2016b-Python-2.7.12.eb --- .../e/Eigen/Eigen-3.2.9-intel-2016b.eb | 13 ++++++++++ ...nieigen-0.5.3-intel-2016b-Python-2.7.12.eb | 26 +++++++++++++++++++ 2 files changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-intel-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-intel-2016b.eb new file mode 100644 index 0000000000..887c3a69f7 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-intel-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.9' + +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': 'intel', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ee0afa54ae --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'minieigen' +version = '0.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://launchpad.net/minieigen/' +description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('Eigen', '3.2.9'), + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/minieigen.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 73d4547c0d9d0fb39175785a409c192867cb6064 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Aug 2016 14:21:46 +0200 Subject: [PATCH 145/701] add easyconfig GDB-7.11.1-intel-2016b-Python-2.7.12.eb --- .../GDB-7.11.1-intel-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.11.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ad51f8adce --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.2.0'), + ('Python', '2.7.12'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' -- GitLab From 70703bb1c7d4994b678d91a77857bd565d97315e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Aug 2016 14:23:10 +0200 Subject: [PATCH 146/701] add easyconfig PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb --- .../g/GLib/GLib-2.49.5-intel-2016b.eb | 33 +++++++++++++++++++ .../g/GTS/GTS-0.7.6-intel-2016b.eb | 25 ++++++++++++++ .../PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++++++ 3 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb new file mode 100644 index 0000000000..cabfe78d32 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.49.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8'), + ('libxml2', '2.9.4'), + ('PCRE', '8.39'), +] + +builddependencies = [('Python', '2.7.12')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016b.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016b.eb new file mode 100644 index 0000000000..53f710cece --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.49.5'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..b961fbd0a4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyGTS' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/projects/pygts/' +description = """ PyGTS is a python package used to construct, manipulate, + and perform computations on triangulated surfaces. + It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('GLib', '2.49.5'), + ('GTS' ,'0.7.6'), +] + +options = {'modulename': 'gts'} + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], + 'dirs':[], +} + +moduleclass = 'vis' -- GitLab From 1ebe33ae913c6208ec1218bd4d99928fc37eaaff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Aug 2016 15:06:32 +0200 Subject: [PATCH 147/701] add easyconfig pkg-config-0.29.1-intel-2016b.eb --- .../pkg-config-0.29.1-intel-2016b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016b.eb new file mode 100644 index 0000000000..57705ced4a --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +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).""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ceb46d68db23cc32e9ce9d1fe5caa2c642fd7152 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Aug 2016 15:27:55 +0200 Subject: [PATCH 148/701] add easyconfig Loki-0.1.7-intel-2016b.eb --- .../l/Loki/Loki-0.1.7-intel-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb new file mode 100644 index 0000000000..a25e47aac4 --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Loki' +version = '0.1.7' + +homepage = 'http://loki-lib.sourceforge.net/' +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and + idioms. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths={ + 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], + 'dirs': ['include/loki'], +} + +moduleclass = 'lib' -- GitLab From fffc70fc2450546956d1d1eea84609628ebb8d9f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 19 Aug 2016 16:30:43 +0200 Subject: [PATCH 149/701] timestamp used as version --- ...oss-2016a.eb => CastXML-20160617-foss-2016a.eb} | 8 ++++---- ...=> pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb} | 14 +++++++------- ...nblas.patch => pyGIMLi-20160803_openblas.patch} | 0 ...> pygccxml-20160706-foss-2016a-Python-3.5.1.eb} | 10 +++++----- ...pyplusplus-20160707-foss-2016a-Python-3.5.1.eb} | 7 ++++--- 5 files changed, 20 insertions(+), 19 deletions(-) rename easybuild/easyconfigs/c/CastXML/{CastXML-d5934bd-foss-2016a.eb => CastXML-20160617-foss-2016a.eb} (78%) rename easybuild/easyconfigs/p/pyGIMLi/{pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb => pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb} (89%) rename easybuild/easyconfigs/p/pyGIMLi/{pyGIMLi-a190c53_openblas.patch => pyGIMLi-20160803_openblas.patch} (100%) rename easybuild/easyconfigs/p/pygccxml/{pygccxml-648e8da-foss-2016a-Python-3.5.1.eb => pygccxml-20160706-foss-2016a-Python-3.5.1.eb} (74%) rename easybuild/easyconfigs/p/pyplusplus/{pyplusplus-2c6c05b7a7d2-foss-2016a-Python-3.5.1.eb => pyplusplus-20160707-foss-2016a-Python-3.5.1.eb} (83%) diff --git a/easybuild/easyconfigs/c/CastXML/CastXML-d5934bd-foss-2016a.eb b/easybuild/easyconfigs/c/CastXML/CastXML-20160617-foss-2016a.eb similarity index 78% rename from easybuild/easyconfigs/c/CastXML/CastXML-d5934bd-foss-2016a.eb rename to easybuild/easyconfigs/c/CastXML/CastXML-20160617-foss-2016a.eb index c326e59979..553587edc6 100644 --- a/easybuild/easyconfigs/c/CastXML/CastXML-d5934bd-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CastXML/CastXML-20160617-foss-2016a.eb @@ -1,16 +1,16 @@ easyblock = 'CMakeMake' name = 'CastXML' -#latest Git commit was: -version = 'd5934bd' +version = '20160617' +commit_id = 'd5934bd' homepage = 'https://github.com/CastXML/CastXML' description = """CastXML is a C-family abstract syntax tree XML output tool.""" toolchain = {'name': 'foss', 'version': '2016a'} -#Only git repository: git clone https://github.com/CastXML/CastXML.git -sources = [SOURCE_TBZ2] +source_urls = ['https://github.com/CastXML/CastXML/archive'] +sources = ['%s.tar.gz' % commit_id] builddependencies = [ ('CMake', '3.4.3'), diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb similarity index 89% rename from easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb rename to easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb index a3b5ad77d1..367c07c748 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb @@ -1,8 +1,8 @@ easyblock = 'CMakeMake' name = 'pyGIMLi' -#latest Git commit was: -version = 'a190c53' +version = '20160803' +commit_id = 'a190c53' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pygimli.org/' @@ -13,8 +13,8 @@ description = """pyGIMLi is an open-source multi-method library for solving inve toolchain = {'name': 'foss', 'version': '2016a'} -#Only git repository: git clone https://github.com/gimli-org/gimli.git a190c53 -sources = [SOURCE_TBZ2] +source_urls = ['https://github.com/gimli-org/gimli/archive/'] +sources = ['%s.tar.gz' % commit_id] patches = ['%(name)s-%(version)s_openblas.patch'] @@ -22,9 +22,9 @@ patches = ['%(name)s-%(version)s_openblas.patch'] #Check scripts/buildThirdParty.sh builddependencies = [ ('CMake', '3.4.3'), - ('CastXML', 'd5934bd'), - ('pygccxml', '648e8da', '-Python-%(pyver)s'), - ('pyplusplus', '2c6c05b7a7d2', '-Python-%(pyver)s'), + ('CastXML', '20160617'), + ('pygccxml', '20160706', '-Python-%(pyver)s'), + ('pyplusplus', '20160707', '-Python-%(pyver)s'), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53_openblas.patch b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803_openblas.patch similarity index 100% rename from easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-a190c53_openblas.patch rename to easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803_openblas.patch diff --git a/easybuild/easyconfigs/p/pygccxml/pygccxml-648e8da-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-3.5.1.eb similarity index 74% rename from easybuild/easyconfigs/p/pygccxml/pygccxml-648e8da-foss-2016a-Python-3.5.1.eb rename to easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-3.5.1.eb index fe4101769f..be70419f92 100644 --- a/easybuild/easyconfigs/p/pygccxml/pygccxml-648e8da-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-3.5.1.eb @@ -1,7 +1,8 @@ easyblock = 'PythonPackage' name = 'pygccxml' -version = '648e8da' +version = '20160706' +commit_id = '648e8da' versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/pygccxml' @@ -9,12 +10,12 @@ description = """Python package for easy C++ declarations navigation.""" toolchain = {'name': 'foss', 'version': '2016a'} -#github source: git clone https://github.com/gccxml/pygccxml.git 648e8da -sources = [SOURCE_TBZ2] +source_urls = ['https://github.com/gccxml/pygccxml/archive/'] +sources = ['%s.tar.gz' % commit_id] dependencies = [ ('Python', '3.5.1'), - ('CastXML', 'd5934bd'), + ('CastXML', '20160617'), ] use_pip = True @@ -27,4 +28,3 @@ sanity_check_paths = { options = {'modulename': '%(name)s'} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-2c6c05b7a7d2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb similarity index 83% rename from easybuild/easyconfigs/p/pyplusplus/pyplusplus-2c6c05b7a7d2-foss-2016a-Python-3.5.1.eb rename to easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb index 9b9fa05275..98760a6c19 100644 --- a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-2c6c05b7a7d2-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb @@ -1,7 +1,8 @@ easyblock = 'PythonPackage' name = 'pyplusplus' -version = '2c6c05b7a7d2' +version = '20160707' +commit_id = '2c6c05b7a7d2' versionsuffix = '-Python-%(pyver)s' homepage = 'https://bitbucket.org/ompl/pyplusplus' @@ -12,11 +13,11 @@ description = """Py++ is a code generator for Boost.Python that simplifies toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://bitbucket.org/ompl/pyplusplus/get/'] -sources = ['%(version)s.zip'] +sources = ['%s.zip' % commit_id] dependencies = [ ('Python', '3.5.1'), - ('pygccxml', '648e8da', '-Python-%(pyver)s'), + ('pygccxml', '20160706', '-Python-%(pyver)s'), ] use_pip = True -- GitLab From 8ae3a6224ce6971badc30396ff7ff60cb706ccb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Aug 2016 16:58:55 +0200 Subject: [PATCH 150/701] add easyconfig X11-20160819-intel-2016b.eb --- .../x/X11/X11-20160819-intel-2016b.eb | 144 ++++++++++++++++++ 1 file changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb new file mode 100644 index 0000000000..9e88299a84 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -0,0 +1,144 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20160819' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'intel', 'version': '2016b'} + +builddependencies = [ + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), +] + +# Python is required for xcb-proto +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +# all extensions can be installed with configure/make/make install +exts_defaultclass = 'ConfigureMake' + +preconfigopts = "if [ -f autogen.sh ]; then ./autogen.sh; fi && " +#preconfigopts += "CPATH=%(installdir)s/include LIBRARY_PATH=%(installdir)s/lib " +#preconfigopts += "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig" + +exts_list = [ + ('xorg-macros', '1.19.0', { + 'source_urls': ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'], + 'source_tmpl': 'util-macros-%(version)s.tar.gz', + }), + ('fixesproto', '5.0', { + 'source_urls': [XORG_PROTO_SOURCE], + }), + ('glproto', '1.4.17', { + 'source_urls': [XORG_PROTO_SOURCE], + }), + ('xextproto', '7.3.0', { + 'source_urls': [XORG_PROTO_SOURCE], + }), + ('xcb-proto', '1.11', { + 'source_urls': ['http://xcb.freedesktop.org/dist/'], + }), + ('inputproto', '2.3.1', { + 'source_urls': [XORG_PROTO_SOURCE], + }), + ('xproto', '7.0.28', { + 'source_urls': [XORG_PROTO_SOURCE], + }), + ('libpthread-stubs', '0.3', { + 'source_urls': ['http://xcb.freedesktop.org/dist/'], + }), + ('kbproto', '1.0.7', { + 'source_urls': [XORG_PROTO_SOURCE], + }), + ('xtrans', '1.3.5', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('xineramaproto', '1.2.1', { + 'source_urls': [XORG_PROTO_SOURCE], + }), + ('randrproto', '1.5.0', { + 'source_urls': [XORG_PROTO_SOURCE], + }), + ('renderproto', '0.11', { + 'source_urls': [XORG_PROTO_SOURCE], + }), + ('libXau', '1.0.8', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libxcb', '1.11.1', { + 'source_urls': ['http://xcb.freedesktop.org/dist/'], + }), + ('xcb-util', '0.4.0', { + 'source_urls': ['http://xcb.freedesktop.org/dist/'], + }), + ('xcb-util-image', '0.4.0', { + 'source_urls': ['http://xcb.freedesktop.org/dist/'], + }), + ('xcb-util-keysyms', '0.4.0', { + 'source_urls': ['http://xcb.freedesktop.org/dist/'], + }), + ('xcb-util-renderutil', '0.3.9', { + 'source_urls': ['http://xcb.freedesktop.org/dist/'], + }), + ('xcb-util-wm', '0.4.1', { + 'source_urls': ['http://xcb.freedesktop.org/dist/'], + }), + ('libxkbcommon', '0.6.1', { + 'source_urls': ['http://xkbcommon.org/download/'], + 'source_tmpl': 'libxkbcommon-%(version)s.tar.xz', + }), + ('libX11', '1.6.3', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libXrender', '0.9.9', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libICE', '1.0.9', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libSM', '1.2.2', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libXt', '1.1.5', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libXext', '1.3.3', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libXfixes', '5.0.2', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libXi', '1.7.6', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libXcursor', '1.1.14', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libXinerama', '1.1.3', { + 'source_urls': [XORG_LIB_SOURCE], + }), + ('libXrandr', '1.5.0', { + 'source_urls': [XORG_LIB_SOURCE], + }), +] + +modextrapaths = { + 'ACLOCAL_PATH': ['share/aclocal'], + 'CPATH': ['include'], + 'LIBRARY_PATH': ['lib'], + 'PKG_CONFIG_PATH': ['lib/pkgconfig', 'share/pkgconfig'], +} + +# 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': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib', + 'lib/python%s/site-packages/xcbgen' % pyshortver, 'lib/pkgconfig', 'share/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From cddde54f320a0efc2b0382218b85c496a7eb9a16 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 19 Aug 2016 12:18:01 -0500 Subject: [PATCH 151/701] Removing SOLAR-Eclipse from this PR --- .../s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb diff --git a/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb b/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb deleted file mode 100644 index 7eccd82679..0000000000 --- a/easybuild/easyconfigs/s/SOLAR-Eclipse/SOLAR-Eclipse-8.1.1.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Ravi Tripathi -# Email: ravi89@uab.edu - -easyblock = "Tarball" - -name = 'SOLAR-Eclipse' -version = '8.1.1' - -homepage = 'http://solar-eclipse-genetics.org/' -description = """SOLAR-Eclipse is an extensive, flexible -software package for genetic variance components analysis, -including linkage analysis, quantitative genetic analysis, -SNP association analysis (QTN and QTLD), and covariate screening. """ - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['https://www.nitrc.org/frs/download.php/8542/'] -sources = ['solar_linux.tar.gz'] - -checksums = ['cbc05fb6c39853a888d9ee151a383461'] - -postinstallcmds = ["./install_solar %(installdir)s %(installdir)s", - "./install_rlwrap %(installdir)s"] - -modextravars = {'SOLAR_BIN': '%(installdir)s/bin', - 'SOLAR_LIB': '%(installdir)s/lib'} -sanity_check_paths = { - 'files': ["bin/solarmain", "bin/rlwrap"], - 'dirs': ["lib", ] -} - -moduleclass = 'bio' - -- GitLab From 60c1274c76c920c528e72ebe4b00f9f347a71ab9 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 19 Aug 2016 12:19:23 -0500 Subject: [PATCH 152/701] Reshuffling of lines in Easyconfig --- easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb index 0075d9362a..1e7fda13a1 100644 --- a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb +++ b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb @@ -16,10 +16,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} #from https://www.nitrc.org/frs/?group_id=370 sources = ['ashs_Linux64_%(version)s.tgz'] -modextravars = {'ASHS_ROOT': '%(installdir)s'} - checksums= ["07fea2883b856af8797b200212b72e71"] +modextravars = {'ASHS_ROOT': '%(installdir)s'} + sanity_check_paths = { 'files': ["bin/ashs_main.sh", "bin/ashs_template_qsub.sh", "bin/ashs_train.sh", "bin/ashs_util_makepdf.sh"], -- GitLab From 04a55b4f87569980bd30834d3012520bdecd93e1 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Fri, 19 Aug 2016 12:22:10 -0500 Subject: [PATCH 153/701] Reshuffling of lines in Easyconfig and removing hardcoding for version --- easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb index e769a35218..b78da99d83 100644 --- a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb +++ b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb @@ -14,12 +14,13 @@ next-generation sequencing machines. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://sourceforge.net/projects/maq/files/maq/0.7.0/'] +source_urls = ['https://sourceforge.net/projects/maq/files/maq/%(version)s/'] sources = ['maq-%(version)s_x86_64-linux.tar.bz2'] +checksums= ["65edff1529c84783d0a4b9208a91efa9"] + modextrapaths = {'PATH': ''} -checksums= ["65edff1529c84783d0a4b9208a91efa9"] sanity_check_paths = { 'files': ["asub", "maq", "maq.pdf", "maq.1", "solid2fastq.pl"], 'dirs': [] -- GitLab From 33f33c068ca5be5abd04ad912ae2a85cf43cf119 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 22 Aug 2016 09:08:37 +0200 Subject: [PATCH 154/701] Missing star (changed directory name) --- .../p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb index 367c07c748..71cea0004f 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb @@ -50,7 +50,7 @@ configopts += '-DPYPLUSPLUS_PATH=$EBROOTPYPLUSPLUS/lib/python%(pyshortver)s/site buildopts = 'gimli pygimli apps' preinstallopts = 'mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages ' -preinstallopts += '&& cp -a ../gimli/python/. %(installdir)s/lib/python%(pyshortver)s/site-packages ' +preinstallopts += '&& cp -a ../gimli*/python/. %(installdir)s/lib/python%(pyshortver)s/site-packages ' preinstallopts += '&& cp -a ../easybuild_obj/lib/. %(installdir)s/lib/ ' preinstallopts += '&& mkdir %(installdir)s/bin ' preinstallopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin ||' -- GitLab From 27ae53c728bd250145c1d873b7135c148acabecd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 22 Aug 2016 13:37:27 +0200 Subject: [PATCH 155/701] Update mympingpong to 0.7.1 and intel/2016b --- ...0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb | 34 +++++++++++++++++++ .../lxml-3.6.4-intel-2016b-Python-2.7.12.eb | 26 ++++++++++++++ ...ntel-2016b-Python-2.7.12-timed-pingpong.eb | 34 +++++++++++++++++++ ...ingpong-0.7.1-intel-2016b-Python-2.7.12.eb | 33 ++++++++++++++++++ ...gconfig-1.1.0-intel-2016b-Python-2.7.12.eb | 26 ++++++++++++++ ...ntel-2016b-Python-2.7.12-vsc-base-2.5.1.eb | 32 +++++++++++++++++ 6 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-3.6.4-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb create mode 100644 easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12-vsc-base-2.5.1.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb new file mode 100644 index 0000000000..027c8b1e43 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.6.0' + +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': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.17' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.6.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/lxml/lxml-3.6.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2329541fb3 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.6.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '3.6.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('Python', '2.7.12'), + ('libxml2', '2.9.4'), + ('libxslt', '1.1.29'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb new file mode 100644 index 0000000000..e2e1da4cf2 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3.1' +label = 'timed-pingpong' +versionsuffix = '-Python-%%(pyver)s-%s' % label + +homepage = 'https://bitbucket.org/mpi4py/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': 'intel', 'version': '2016b'} + +source_urls = [BITBUCKET_DOWNLOADS] +sources = [SOURCE_TAR_GZ] + +patches = ['mpi4py-%%(version)s_%s.patch' % label] + +dependencies = [('Python', '2.7.12')] + +# force rebuilding everything, including patched files +buildopts = '--force' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'], +} + +# check that timed pingpong routines that are added via the patch are available +sanity_check_commands = [ + ('python', '-c "from mpi4py.MPI import Comm; import sys; sys.exit((1, 0)[\'PingpongRS\' in dir(Comm)])"'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..6d9e013cda --- /dev/null +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'mympingpong' +version = '0.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/mympingpong' +description = """A mpi4py based random pair pingpong network stress test.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +vsc_base_ver = '2.5.1' +dependencies = [ + ('Python', '2.7.12'), + ('vsc-base', vsc_base_ver, versionsuffix), + ('vsc-mympirun', '3.4.3', versionsuffix + '-vsc-base-%s' % vsc_base_ver), + ('matplotlib', '1.5.1', versionsuffix), + ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.17'), + ('mpi4py', '1.3.1', versionsuffix + '-timed-pingpong'), + ('lxml', '3.6.4', versionsuffix), +] + +options = {'modulename': 'vsc.mympingpong'} + +sanity_check_paths = { + 'files': ['bin/mympingpong', 'bin/mympingponganalysis'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..5be193eb6b --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('pkg-config', '0.29.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12-vsc-base-2.5.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12-vsc-base-2.5.1.eb new file mode 100755 index 0000000000..4c57127480 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12-vsc-base-2.5.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '3.4.3' + +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] + +vsc_base_ver = '2.5.1' +versionsuffix = '-Python-%%(pyver)s-vsc-base-%s' % vsc_base_ver + +dependencies = [ + ('Python', '2.7.12'), + ('vsc-base', vsc_base_ver, '-Python-%(pyver)s'), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +options = {'modulename': 'vsc.mympirun'} + +sanity_check_paths = { + 'files': ['bin/mympirun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From 81446b97ca3d3b435cd8936e9b121b04c869d371 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 22 Aug 2016 13:54:18 +0200 Subject: [PATCH 156/701] Stacks 1.42 compiled with the foss 2016a toolchain. --- .../s/Stacks/Stacks-1.42-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb new file mode 100644 index 0000000000..6d5d6358c8 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.42' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose + of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), + ('sparsehash', '2.0.2'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From efd9c611e344b8ea41ce0ea0ca0c47289898e266 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 22 Aug 2016 13:58:09 +0200 Subject: [PATCH 157/701] Drop vsc-base suffix for mympirun --- ...ingpong-0.7.1-intel-2016b-Python-2.7.12.eb | 2 +- ...ntel-2016b-Python-2.7.12-vsc-base-2.5.1.eb | 32 ------------------- 2 files changed, 1 insertion(+), 33 deletions(-) delete mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12-vsc-base-2.5.1.eb diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb index 6d9e013cda..4f094313bb 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb @@ -16,7 +16,7 @@ vsc_base_ver = '2.5.1' dependencies = [ ('Python', '2.7.12'), ('vsc-base', vsc_base_ver, versionsuffix), - ('vsc-mympirun', '3.4.3', versionsuffix + '-vsc-base-%s' % vsc_base_ver), + ('vsc-mympirun', '3.4.3', versionsuffix), ('matplotlib', '1.5.1', versionsuffix), ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.17'), ('mpi4py', '1.3.1', versionsuffix + '-timed-pingpong'), diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12-vsc-base-2.5.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12-vsc-base-2.5.1.eb deleted file mode 100755 index 4c57127480..0000000000 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12-vsc-base-2.5.1.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'vsc-mympirun' -version = '3.4.3' - -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.""" - -toolchain = {'name': 'intel', 'version': '2016b'} - -sources = [SOURCE_TAR_GZ] -source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] - -vsc_base_ver = '2.5.1' -versionsuffix = '-Python-%%(pyver)s-vsc-base-%s' % vsc_base_ver - -dependencies = [ - ('Python', '2.7.12'), - ('vsc-base', vsc_base_ver, '-Python-%(pyver)s'), -] - -# we ship something in bin/fake -modextrapaths = {'PATH': 'bin/fake'} - -options = {'modulename': 'vsc.mympirun'} - -sanity_check_paths = { - 'files': ['bin/mympirun'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' -- GitLab From 108c8724f5cd0c0af8d30703d5ac35e4e461d3f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2016 15:01:25 +0200 Subject: [PATCH 158/701] add checksums in easyconfig for QuantumESPRESSO 5.1.2, remove plumed from list of buildopts --- .../QuantumESPRESSO-5.1.2-ictce-7.3.5.eb | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb index 66a93062f3..d453b22ecb 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb @@ -27,7 +27,18 @@ source_urls = [ 'http://www.qe-forge.org/gf/download/frsrelease/185/754/', # GWW-5.1.2.tar.gz ] -buildopts = 'all plumed w90 want gipaw' +checksums = [ + '55f766d1c41c8e7994b0d6717a55c3ea', # espresso-5.1.2.tar.gz + '77ec8a5b2106abc080a55463d4fc964b', # atomic-5.1.2.tar.gz + 'b6123aa99f7db958dd635e9837abdf00', # neb-5.1.2.tar.gz + '49c65d222449c5fcea539470e8001170', # PHonon-5.1.2.tar.gz + '6a6c8f84d2a3e65d60cf4e5387383b9b', # pwcond-5.1.2.tar.gz + '9790e7d55fc1f08c554a9d0212bc7f9e', # tddfpt-5.1.2.tar.gz + 'c27d6c9515c0ce29462a9b1e8203d118', # xspectra-5.1.2.tar.gz + '681c7f83b4adefbf2da721c4b8210670', # GWW-5.1.2.tar.gz +] + +buildopts = 'all w90 want gipaw' # parallel build tends to fail parallel = 1 -- GitLab From 1b6dd5fcceba0c0a9b7808904d6958794a71cd18 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 22 Aug 2016 15:59:12 +0200 Subject: [PATCH 159/701] Add missing dep to mympingpong --- .../h/hwloc/hwloc-1.11.3-intel-2016b.eb | 23 +++++++++++++++++++ ...ingpong-0.7.1-intel-2016b-Python-2.7.12.eb | 1 + .../n/numactl/numactl-2.0.11-intel-2016b.eb | 23 +++++++++++++++++++ 3 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016b.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb new file mode 100644 index 0000000000..651e1648ba --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +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': 'intel', 'version': '2016b'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb index 4f094313bb..6be49aff6f 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb @@ -21,6 +21,7 @@ dependencies = [ ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.17'), ('mpi4py', '1.3.1', versionsuffix + '-timed-pingpong'), ('lxml', '3.6.4', versionsuffix), + ('hwloc', '1.11.3'), ] options = {'modulename': 'vsc.mympingpong'} diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016b.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016b.eb new file mode 100644 index 0000000000..0c6c854f4a --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +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': 'intel', 'version': '2016b'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' -- GitLab From 80c1b1656c50cadb9971560561e9d0900f13f5d1 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 22 Aug 2016 16:13:06 +0200 Subject: [PATCH 160/701] lua syntax fixed, unnecessary comments removed --- .../Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb index 93d2f1fa5c..300ae8a70c 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb @@ -25,7 +25,6 @@ dependencies = [ with_configure = 'True' configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" ' -#configopts = 'CC=$CC_SEQ MPICC=$CC CPPFLAGS="" FCFLAGS="-nofor_main" ' configopts += '--with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" ' configopts += '--with-fft-libs="$LIBFFT" ' @@ -49,6 +48,6 @@ sanity_check_paths = { # is twice in the PATH. Withouth removing the QuantumESPRESSO one, this version of Yambo would be used, # because it is earlier in the PATH modtclfooter = "remove-path PATH $::env(EBROOTQUANTUMESPRESSO)/espresso-%s/YAMBO/bin" % qever -modluafooter = 'remove_path("PATH", os.getenv(EBROOTQUANTUMESPRESSO) .. "/espresso-%s/YAMBO/bin")' % qever +modluafooter = 'remove_path("PATH", os.getenv("EBROOTQUANTUMESPRESSO") .. "/espresso-%s/YAMBO/bin")' % qever moduleclass = 'phys' -- GitLab From 90239d4c89d00b98de5a857e1ebf436e8ba63785 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2016 16:42:04 +0200 Subject: [PATCH 161/701] add easyconfig BEDTools-2.26.0-intel-2016b.eb, add easyconfig SAMtools-1.3.1-intel-2016b.eb --- .../b/BEDTools/BEDTools-2.26.0-intel-2016b.eb | 33 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.3.1-intel-2016b.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2016b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2016b.eb new file mode 100644 index 0000000000..3c9d695141 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2016b.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.26.0' + +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': 'intel', 'version': '2016b'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['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' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb new file mode 100644 index 0000000000..068f81d41a --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.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 +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +## +name = 'SAMtools' +version = '1.3.1' + +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': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-%(version)s_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' -- GitLab From 44af07a089e1f0f732f86d9c14d5add559c1c61d Mon Sep 17 00:00:00 2001 From: Appmaint Date: Mon, 22 Aug 2016 16:58:18 +0100 Subject: [PATCH 162/701] ABINIT 7.6.2 w/ patches --- .../a/ABINIT/ABINIT-7.6.2-foss-2015a.eb | 35 +++++++++++++++++++ .../ABINIT/ABINIT-7.6.2_named-constant.patch | 16 +++++++++ .../a/ABINIT/ABINIT-7.6.2_odamix.patch | 11 ++++++ 3 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb new file mode 100644 index 0000000000..b50c69f2c4 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb @@ -0,0 +1,35 @@ +easyblock = "ConfigureMake" + +name = 'ABINIT' +version = '7.6.2' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '--enable-mpi --with-mpi-prefix="$EBROOTOPENMPI" --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib64 -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor=netcdf+etsf_io --with-dft-flavor=libxc --enable-gw-dpc' + +patches = ['ABINIT-7.6.2_named-constant.patch', + 'ABINIT-7.6.2_odamix.patch', +] + +dependencies = [ + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch new file mode 100644 index 0000000000..612de708f5 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch @@ -0,0 +1,16 @@ +--- src/62_ctqmc/defs.h.orig 2014-02-15 21:30:20.000000000 +0000 ++++ src/62_ctqmc/defs.h 2016-08-22 13:05:09.473620286 +0100 +@@ -5,11 +5,11 @@ + + #define MALLOC(ARR,SIZE) ABI_ALLOCATE(ARR,SIZE) + #define FREE(ARR) ABI_DEALLOCATE(ARR) +-#define FREEIF(ARR) IF(ALLOCATED(ARR)) THEN NEWLINE ABI_DEALLOCATE(ARR) NEWLINE END IF ++#define FREEIF(ARR) IF(ALLOCATED(ARR)) ABI_DEALLOCATE(ARR) + + #define DT_MALLOC(ARR,SIZE) ABI_DATATYPE_ALLOCATE(ARR,SIZE) + #define DT_FREE(ARR) ABI_DATATYPE_DEALLOCATE(ARR) +-#define DT_FREEIF(ARR) IF(ALLOCATED(ARR)) THEN NEWLINE ABI_DATATYPE_DEALLOCATE(ARR) NEWLINE END IF ++#define DT_FREEIF(ARR) IF(ALLOCATED(ARR)) ABI_DATATYPE_DEALLOCATE(ARR) + + #define myWARNALL(msg) MSG_WARNING(msg) + #define myWARN(msg) call msg_hndl(msg,"WARNING","PERS") diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch new file mode 100644 index 0000000000..0c5fe6dcf3 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch @@ -0,0 +1,11 @@ +--- src/67_common/odamix.F90.orig 2016-08-22 13:27:30.289621140 +0100 ++++ src/67_common/odamix.F90 2016-08-22 13:27:40.063570238 +0100 +@@ -544,7 +544,7 @@ + do ispden=1,pawrhoij(iatom)%nspden + do irhoij=1,pawrhoij(iatom)%nrhoijsel + klmn=2*pawrhoij(iatom)%rhoijselect(irhoij)-1 +- rhoijtmp(klmn-1:klmn+1,ispden)=pawrhoij(iatom)%rhoijp(jrhoij:jrhoij+1,ispden) ++ rhoijtmp(klmn:klmn+1,ispden)=pawrhoij(iatom)%rhoijp(jrhoij:jrhoij+1,ispden) + jrhoij=jrhoij+2 + end do + end do -- GitLab From 844956b9cea0478d994ba0187cd04c632f88797e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2016 18:14:20 +0200 Subject: [PATCH 163/701] switch to using older toolchain intel/2015a, add easyconfigs for missing deps --- ...=> nco-0.0.2-intel-2015a-Python-2.7.10.eb} | 6 ++--- ...-python-1.2.2-intel-2015a-Python-2.7.10.eb | 24 +++++++++++++++++ .../numpy-1.10.4-intel-2015a-Python-2.7.10.eb | 26 +++++++++++++++++++ .../scipy-0.16.1-intel-2015a-Python-2.7.10.eb | 19 ++++++++++++++ 4 files changed, 72 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/n/nco/{nco-0.0.2-intel-2016a-Python-2.7.11.eb => nco-0.0.2-intel-2015a-Python-2.7.10.eb} (82%) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015a-Python-2.7.10.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.16.1-intel-2015a-Python-2.7.10.eb diff --git a/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2015a-Python-2.7.10.eb similarity index 82% rename from easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2015a-Python-2.7.10.eb index 0732494447..a661d2786b 100644 --- a/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2015a-Python-2.7.10.eb @@ -7,15 +7,15 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/nco/pynco' description = """Python bindings for NCO""" -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ - ('Python', '2.7.11'), - ('NCO', '4.4.9', versionsuffix), + ('Python', '2.7.10'), + ('NCO', '4.5.1', versionsuffix), ('numpy', '1.10.4', versionsuffix), ('scipy', '0.16.1', versionsuffix), ('netcdf4-python', '1.2.2', versionsuffix), diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..9a718367a9 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,24 @@ +name = 'netcdf4-python' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] +sources = ['v%(version)srel.tar.gz'] + +patches = ['netcdf4-python-%(version)s-avoid-diskless-test.patch'] + +dependencies = [ + ('Python', '2.7.10'), + ('numpy', '1.10.4', versionsuffix), + ('HDF5', '1.8.13'), + ('netCDF', '4.3.2'), + ('cURL', '7.43.0'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..d197dabcbd --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.10.4' +versionsuffix = '-Python-%(pyver)s' + +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', + 'numpy-%(version)s-sse42.patch', +] + +dependencies = [ + ('Python', '2.7.10'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.16.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/scipy/scipy-0.16.1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000..6126cbe489 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.16.1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.16.1' +versionsuffix = '-Python-2.7.10' + +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', '1.10.4', versionsuffix), +] + +moduleclass = 'math' -- GitLab From 506bcf09eb1e6923baf8116a9a11c6b4f01a8847 Mon Sep 17 00:00:00 2001 From: Liang Date: Mon, 22 Aug 2016 18:26:16 +0200 Subject: [PATCH 164/701] Patch file name changed --- .../QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 2 +- .../QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch | 12 ++++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index 9c0424411c..57849d2efa 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -46,7 +46,7 @@ source_urls = [ # Hybrid option exists only for backward compatibility, use toolchain option openmp instead. hybrid = True # Patch file to avoid the CPP problem generated by different OSes -patches = ['QE_gfortran_f90rule.patch'] +patches = ['QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch'] # packages included in 5.4.0 version of QE. We met errors when try to include gipaw, yambo and someother packages. buildopts = 'all tddfpt neb xspectra ph ' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch new file mode 100644 index 0000000000..85d62f606b --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch @@ -0,0 +1,12 @@ +diff -rupN espresso-5.4.0.orig/install/make.sys.in espresso-5.4.0/install/make.sys.in +--- espresso-5.4.0.orig/install/make.sys.in 2016-04-24 23:19:25.000000000 +0200 ++++ espresso-5.4.0/install/make.sys.in 2016-06-11 15:08:15.869499000 +0200 +@@ -13,7 +13,7 @@ + # remember the tabulator in the first column !!! + + .f90.o: +- @f90rule@ ++ $(MPIF90) $(F90FLAGS) -c $< + + # .f.o and .c.o: do not modify + -- GitLab From 1b63f9a6a91cb3274ab6cd540598e599986864e2 Mon Sep 17 00:00:00 2001 From: Liang Date: Mon, 22 Aug 2016 18:28:13 +0200 Subject: [PATCH 165/701] Patch file renamed --- .../q/QuantumESPRESSO/QE_gfortran_f90rule.patch | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QE_gfortran_f90rule.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QE_gfortran_f90rule.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QE_gfortran_f90rule.patch deleted file mode 100644 index 85d62f606b..0000000000 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QE_gfortran_f90rule.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -rupN espresso-5.4.0.orig/install/make.sys.in espresso-5.4.0/install/make.sys.in ---- espresso-5.4.0.orig/install/make.sys.in 2016-04-24 23:19:25.000000000 +0200 -+++ espresso-5.4.0/install/make.sys.in 2016-06-11 15:08:15.869499000 +0200 -@@ -13,7 +13,7 @@ - # remember the tabulator in the first column !!! - - .f90.o: -- @f90rule@ -+ $(MPIF90) $(F90FLAGS) -c $< - - # .f.o and .c.o: do not modify - -- GitLab From 27357c078f114794d74a66e29c325f31f81b3e04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2016 18:49:01 +0200 Subject: [PATCH 166/701] use existing patch for netcdf4-python 1.2.2 --- .../netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb index 9a718367a9..a0171e055b 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb @@ -11,7 +11,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] sources = ['v%(version)srel.tar.gz'] -patches = ['netcdf4-python-%(version)s-avoid-diskless-test.patch'] +patches = ['netcdf4-python-1.1.8-avoid-diskless-test.patch'] dependencies = [ ('Python', '2.7.10'), -- GitLab From 906e4d0627ff23e9031329b5f699ae08dcb77f76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2016 18:56:03 +0200 Subject: [PATCH 167/701] fix netCDF/HDF5 version conflict in deps for nco --- .../netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb index a0171e055b..1c992d8b51 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb @@ -16,8 +16,8 @@ patches = ['netcdf4-python-1.1.8-avoid-diskless-test.patch'] dependencies = [ ('Python', '2.7.10'), ('numpy', '1.10.4', versionsuffix), - ('HDF5', '1.8.13'), - ('netCDF', '4.3.2'), + ('HDF5', '1.8.15'), + ('netCDF', '4.3.3.1'), ('cURL', '7.43.0'), ] -- GitLab From c7e8ea90e9eddf010973a7bd8b35f362a94bf253 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2016 19:21:32 +0200 Subject: [PATCH 168/701] change X11 easyconfig according to updated Bundle easyblock --- .../x/X11/X11-20160819-intel-2016b.eb | 171 +++++++----------- 1 file changed, 61 insertions(+), 110 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb index 9e88299a84..e4450735c2 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -8,129 +8,80 @@ description = "The X Window System (X11) is a windowing system for bitmap displa toolchain = {'name': 'intel', 'version': '2016b'} +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + builddependencies = [ ('Autotools', '20150215'), ('pkg-config', '0.29.1'), ] +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.0', { + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('fixesproto', '5.0', common_specs), + ('glproto', '1.4.17', common_specs), + ('xextproto', '7.3.0', common_specs), + ('xcb-proto', '1.11', common_specs), + ('inputproto', '2.3.1', common_specs), + ('xproto', '7.0.28', common_specs), + ('libpthread-stubs', '0.3', common_specs), + ('kbproto', '1.0.7', common_specs), + ('xtrans', '1.3.5', common_specs), + ('xineramaproto', '1.2.1', common_specs), + ('randrproto', '1.5.0', common_specs), + ('renderproto', '0.11', common_specs), + ('libXau', '1.0.8', common_specs), + ('libxcb', '1.11.1', common_specs), + ('xcb-util', '0.4.0', common_specs), + ('xcb-util-image', '0.4.0', common_specs), + ('xcb-util-keysyms', '0.4.0', common_specs), + ('xcb-util-renderutil', '0.3.9', common_specs), + ('xcb-util-wm', '0.4.1', common_specs), + ('libxkbcommon', '0.6.1', { + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.3', common_specs), + ('libXrender', '0.9.9', common_specs), + ('libICE', '1.0.9', common_specs), + ('libSM', '1.2.2', common_specs), + ('libXt', '1.1.5', common_specs), + ('libXext', '1.3.3', common_specs), + ('libXfixes', '5.0.2', common_specs), + ('libXi', '1.7.6', common_specs), + ('libXcursor', '1.1.14', common_specs), + ('libXinerama', '1.1.3', common_specs), + ('libXrandr', '1.5.0', common_specs), +] + # Python is required for xcb-proto allow_system_deps = [('Python', SYS_PYTHON_VERSION)] pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) -# all extensions can be installed with configure/make/make install -exts_defaultclass = 'ConfigureMake' - preconfigopts = "if [ -f autogen.sh ]; then ./autogen.sh; fi && " #preconfigopts += "CPATH=%(installdir)s/include LIBRARY_PATH=%(installdir)s/lib " #preconfigopts += "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig" -exts_list = [ - ('xorg-macros', '1.19.0', { - 'source_urls': ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'], - 'source_tmpl': 'util-macros-%(version)s.tar.gz', - }), - ('fixesproto', '5.0', { - 'source_urls': [XORG_PROTO_SOURCE], - }), - ('glproto', '1.4.17', { - 'source_urls': [XORG_PROTO_SOURCE], - }), - ('xextproto', '7.3.0', { - 'source_urls': [XORG_PROTO_SOURCE], - }), - ('xcb-proto', '1.11', { - 'source_urls': ['http://xcb.freedesktop.org/dist/'], - }), - ('inputproto', '2.3.1', { - 'source_urls': [XORG_PROTO_SOURCE], - }), - ('xproto', '7.0.28', { - 'source_urls': [XORG_PROTO_SOURCE], - }), - ('libpthread-stubs', '0.3', { - 'source_urls': ['http://xcb.freedesktop.org/dist/'], - }), - ('kbproto', '1.0.7', { - 'source_urls': [XORG_PROTO_SOURCE], - }), - ('xtrans', '1.3.5', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('xineramaproto', '1.2.1', { - 'source_urls': [XORG_PROTO_SOURCE], - }), - ('randrproto', '1.5.0', { - 'source_urls': [XORG_PROTO_SOURCE], - }), - ('renderproto', '0.11', { - 'source_urls': [XORG_PROTO_SOURCE], - }), - ('libXau', '1.0.8', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libxcb', '1.11.1', { - 'source_urls': ['http://xcb.freedesktop.org/dist/'], - }), - ('xcb-util', '0.4.0', { - 'source_urls': ['http://xcb.freedesktop.org/dist/'], - }), - ('xcb-util-image', '0.4.0', { - 'source_urls': ['http://xcb.freedesktop.org/dist/'], - }), - ('xcb-util-keysyms', '0.4.0', { - 'source_urls': ['http://xcb.freedesktop.org/dist/'], - }), - ('xcb-util-renderutil', '0.3.9', { - 'source_urls': ['http://xcb.freedesktop.org/dist/'], - }), - ('xcb-util-wm', '0.4.1', { - 'source_urls': ['http://xcb.freedesktop.org/dist/'], - }), - ('libxkbcommon', '0.6.1', { - 'source_urls': ['http://xkbcommon.org/download/'], - 'source_tmpl': 'libxkbcommon-%(version)s.tar.xz', - }), - ('libX11', '1.6.3', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libXrender', '0.9.9', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libICE', '1.0.9', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libSM', '1.2.2', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libXt', '1.1.5', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libXext', '1.3.3', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libXfixes', '5.0.2', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libXi', '1.7.6', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libXcursor', '1.1.14', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libXinerama', '1.1.3', { - 'source_urls': [XORG_LIB_SOURCE], - }), - ('libXrandr', '1.5.0', { - 'source_urls': [XORG_LIB_SOURCE], - }), -] - -modextrapaths = { - 'ACLOCAL_PATH': ['share/aclocal'], - 'CPATH': ['include'], - 'LIBRARY_PATH': ['lib'], - 'PKG_CONFIG_PATH': ['lib/pkgconfig', 'share/pkgconfig'], -} +#modextrapaths = { +# 'ACLOCAL_PATH': ['share/aclocal'], +# 'CPATH': ['include'], +# 'LIBRARY_PATH': ['lib'], +# 'PKG_CONFIG_PATH': ['lib/pkgconfig', 'share/pkgconfig'], +#} # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -- GitLab From 14e0fb39737ef95d7c33aa13154a9883dace0f36 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2016 19:23:46 +0200 Subject: [PATCH 169/701] remove commented out lines --- easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb index e4450735c2..c7b4981705 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -73,15 +73,6 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) preconfigopts = "if [ -f autogen.sh ]; then ./autogen.sh; fi && " -#preconfigopts += "CPATH=%(installdir)s/include LIBRARY_PATH=%(installdir)s/lib " -#preconfigopts += "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig" - -#modextrapaths = { -# 'ACLOCAL_PATH': ['share/aclocal'], -# 'CPATH': ['include'], -# 'LIBRARY_PATH': ['lib'], -# 'PKG_CONFIG_PATH': ['lib/pkgconfig', 'share/pkgconfig'], -#} # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -- GitLab From 99f1db4c8b33ac5d5fbc57f16f0cecbf91a3d56a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 Aug 2016 10:56:25 +0200 Subject: [PATCH 170/701] Added CP2K/3.0 with psmp build using intel/2016b --- .../b/byacc/byacc-20160606-intel-2016b.eb | 22 ++++++++++ ...a-psmp.eb => CP2K-3.0-intel-2016b-psmp.eb} | 10 ++--- .../easyconfigs/g/GSL/GSL-2.1-intel-2016b.eb | 19 +++++++++ .../g/Guile/Guile-1.8.8-intel-2016b.eb | 32 ++++++++++++++ .../l/Libint/Libint-1.1.6-intel-2016b.eb | 23 ++++++++++ .../libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb | 27 ++++++++++++ .../libmatheval-1.1.11-intel-2016b.eb | 33 +++++++++++++++ .../libunistring-0.9.6-intel-2016b.eb | 24 +++++++++++ .../l/libxc/libxc-3.0.0-intel-2016b.eb | 31 ++++++++++++++ .../l/libxsmm/libxsmm-1.4.4-intel-2016b.eb | 26 ++++++++++++ .../p/PLUMED/PLUMED-2.2.3-intel-2016b.eb | 42 +++++++++++++++++++ 11 files changed, 284 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/b/byacc/byacc-20160606-intel-2016b.eb rename easybuild/easyconfigs/c/CP2K/{CP2K-3.0-intel-2016a-psmp.eb => CP2K-3.0-intel-2016b-psmp.eb} (87%) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-20160606-intel-2016b.eb b/easybuild/easyconfigs/b/byacc/byacc-20160606-intel-2016b.eb new file mode 100644 index 0000000000..981c94c528 --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20160606-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20160606' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/byacc'] + +checksums = ['d527c811b360f04a8c5f5a0a90625966'] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb similarity index 87% rename from easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb rename to easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb index 15773e8b83..edc9451097 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb @@ -8,7 +8,7 @@ description = """CP2K is a freely available (GPL) program, written in Fortran 95 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': '2016a'} +toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_BZ2] @@ -20,10 +20,10 @@ patches = [ ] dependencies = [ - ('Libint', '1.1.4'), - ('libxc', '2.2.3'), - ('PLUMED', '2.2.2'), - ('libxsmm', '1.4'), + ('Libint', '1.1.6'), + ('libxc', '3.0.0'), + ('PLUMED', '2.2.3'), + ('libxsmm', '1.4.4'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016b.eb new file mode 100644 index 0000000000..5018bf16a6 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.1' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016b.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016b.eb new file mode 100644 index 0000000000..1be1335f08 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016b.eb @@ -0,0 +1,32 @@ +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': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.1'), + ('libunistring', '0.9.6'), + ('pkg-config', '0.29.1'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +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/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb new file mode 100644 index 0000000000..f69e8361ef --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -0,0 +1,23 @@ +name = 'Libint' +version = '1.1.6' + +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': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True, 'optarch': 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.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb new file mode 100644 index 0000000000..11a61b4be8 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesaver = '12.0.0' +versionsuffix = '-Mesa-%s' % mesaver + +dependencies = [ + ('Mesa', mesaver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb new file mode 100644 index 0000000000..1e97665ea8 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('byacc', '20160606'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-intel-2016b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-intel-2016b.eb new file mode 100644 index 0000000000..a1958c52c6 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.6' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb new file mode 100644 index 0000000000..951b7f0605 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.0' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# 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%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-intel-2016b.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-intel-2016b.eb new file mode 100644 index 0000000000..d0e0210103 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.4.4' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/hfp/libxsmm/archive/'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-intel-2016b.eb new file mode 100644 index 0000000000..f53ad8b7b8 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-intel-2016b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.3' + +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': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From 6846deca6416a000dc859a673e8695ba016c0334 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 23 Aug 2016 11:11:00 +0200 Subject: [PATCH 171/701] preinstall -> install --- .../pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb index 71cea0004f..5c868303ad 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb @@ -49,11 +49,10 @@ configopts += '-DPYPLUSPLUS_PATH=$EBROOTPYPLUSPLUS/lib/python%(pyshortver)s/site buildopts = 'gimli pygimli apps' -preinstallopts = 'mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages ' -preinstallopts += '&& cp -a ../gimli*/python/. %(installdir)s/lib/python%(pyshortver)s/site-packages ' -preinstallopts += '&& cp -a ../easybuild_obj/lib/. %(installdir)s/lib/ ' -preinstallopts += '&& mkdir %(installdir)s/bin ' -preinstallopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin ||' +installopts = ' && mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages ' +installopts += '&& cp -a ../gimli*/python/. %(installdir)s/lib/python%(pyshortver)s/site-packages ' +installopts += '&& mkdir %(installdir)s/bin ' +installopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin' sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bms2vtk', 'dc1dinv', 'dc1dsmooth', 'fdem1dinv', 'fdem1dsmooth', -- GitLab From 183cc3196d7d8b4c25c56aff7734919cac82cefe Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 Aug 2016 11:19:35 +0200 Subject: [PATCH 172/701] Drop unneeded easyconfig --- .../libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb deleted file mode 100644 index 11a61b4be8..0000000000 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016a-Mesa-12.0.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libGLU' -version = '9.0.0' - -homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' -description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ - -toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'pic': True} - -source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] -sources = ['glu-%(version)s.tar.bz2'] - -mesaver = '12.0.0' -versionsuffix = '-Mesa-%s' % mesaver - -dependencies = [ - ('Mesa', mesaver), -] - -sanity_check_paths = { - 'files': ['lib/libGLU.so.1'], - 'dirs': [], -} - -moduleclass = 'vis' -- GitLab From 2ea8f56570cfc5dd6b564e8223a447bd3f6afbe1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2016 11:38:12 +0200 Subject: [PATCH 173/701] check for 'configure' rather than 'autogen.sh' --- easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb index c7b4981705..939b3393dd 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -72,7 +72,7 @@ components = [ allow_system_deps = [('Python', SYS_PYTHON_VERSION)] pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) -preconfigopts = "if [ -f autogen.sh ]; then ./autogen.sh; fi && " +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -- GitLab From 2064016535152df4243a0c4ddcb003b3a6f80e07 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 23 Aug 2016 10:41:59 +0100 Subject: [PATCH 174/701] Open MPI 2.0.0 + dependencies hwloc 1.11.3 and numactl 2.0.11 all with toolchain GCC 5.2.0 --- .../h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb | 23 +++++++++++++ .../n/numactl/numactl-2.0.11-GCC-5.2.0.eb | 23 +++++++++++++ .../o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb | 34 +++++++++++++++++++ 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb new file mode 100644 index 0000000000..dc85bdedc2 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +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': 'GCC', 'version': '5.2.0'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.eb new file mode 100644 index 0000000000..9def738efc --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +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': 'GCC', 'version': '5.2.0'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb new file mode 100644 index 0000000000..fb51776cb6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.0' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '5.2.0'} + +sources = [SOURCELOWER_TAR_GZ] + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] + +dependencies = [('hwloc', '1.11.3')] + +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'), ('libpciaccess-devel'), ('libudev-devel', 'systemd-devel'),] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "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] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/c"], +} + +moduleclass = 'mpi' -- GitLab From 3281a9b99bdee4367c3b446a7c9a118a39de2845 Mon Sep 17 00:00:00 2001 From: jhein32 Date: Tue, 23 Aug 2016 12:08:57 +0200 Subject: [PATCH 175/701] mpi4py 2.0.0 version for python 2.7.12 and intel 2016b First attempt --- .../mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ddd5bdaa06 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '2.0.0' + +homepage = 'https://bitbucket.org/mpi4py/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': 'intel', 'version': '2016b'} + +source_urls = [BITBUCKET_DOWNLOADS] +sources = [SOURCE_TAR_GZ] + +py_maj_min = '2.7' +pyver = '%s.12' % py_maj_min +versionsuffix = '-Python-%s' % pyver + +dependencies = [('Python', pyver)] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % py_maj_min], +} + +moduleclass = 'mpi' -- GitLab From 2dbf1160503b9c3130ebb11dc838b976df34eeb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2016 13:21:40 +0200 Subject: [PATCH 176/701] remove trailing whitespace --- .../h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb | 44 +++++++++---------- .../n/numactl/numactl-2.0.11-GCC-5.2.0.eb | 40 ++++++++--------- 2 files changed, 42 insertions(+), 42 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb index dc85bdedc2..ef0b1e1c2c 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.3' - -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': 'GCC', 'version': '5.2.0'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '5.2.0'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.eb index 9def738efc..2c6aa67bd4 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'numactl' -version = '2.0.11' - -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.""" - +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +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': 'GCC', 'version': '5.2.0'} -source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] -sources = [SOURCE_TAR_GZ] - -checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] - -sanity_check_paths = { - 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], - 'dirs': ['share/man', 'include'] -} - +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + moduleclass = 'tools' -- GitLab From 15bc2e243fe223cbceb69575f2044b9b8555fd4b Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 23 Aug 2016 12:48:51 +0100 Subject: [PATCH 177/701] BayPass 2.1 with foss 2015a --- .../b/BayPass/BayPass-2.1-foss-2015a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb new file mode 100644 index 0000000000..bfc37a6d79 --- /dev/null +++ b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'BayPass' +version = '2.1' + +homepage = 'http://www1.montpellier.inra.fr/CBGP/software/baypass/' +description = """The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www1.montpellier.inra.fr/CBGP/software/baypass/files/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +start_dir = 'sources' + +files_to_copy = [(['g_baypass'], 'bin'), (['BayPass_manual_2.1.pdf'], 'manual'), 'examples', 'utils'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/g_baypass'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From dd50cb276e5d3af7ee983f4f096cb5809e7f403d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2016 14:22:03 +0200 Subject: [PATCH 178/701] add easyconfig kallisto-0.43.0-intel-2016b.eb --- .../k/kallisto/kallisto-0.43.0-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.43.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.0-intel-2016b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.0-intel-2016b.eb new file mode 100644 index 0000000000..24e6fb2d59 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.0-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.43.0' + +homepage = 'http://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/pachterlab/kallisto/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.5.2')] +dependencies = [('HDF5', '1.8.17')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6f5d7276bd0f83c2874f9fb64d7f263ce02e55b6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 23 Aug 2016 14:24:24 +0200 Subject: [PATCH 179/701] {math}[binary] MCR R2013a (REVIEW) --- easybuild/easyconfigs/m/MCR/MCR-R2013a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2013a.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb new file mode 100644 index 0000000000..caffaedaa3 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2013a' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_31')] + +moduleclass = 'math' -- GitLab From cab1edec9486083cc3a9d530e09bc87068b293f3 Mon Sep 17 00:00:00 2001 From: jhein32 Date: Tue, 23 Aug 2016 14:41:32 +0200 Subject: [PATCH 180/701] Update for %(pyver)s template --- .../m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb index ddd5bdaa06..b24967a55e 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'mpi4py' version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://bitbucket.org/mpi4py/mpi4py' description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for @@ -12,15 +13,11 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] -py_maj_min = '2.7' -pyver = '%s.12' % py_maj_min -versionsuffix = '-Python-%s' % pyver - -dependencies = [('Python', pyver)] +dependencies = [('Python', '2,7.12')] sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/mpi4py' % py_maj_min], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'], } moduleclass = 'mpi' -- GitLab From 7e43f81038f794b1783231d61d61bc738bbf01ae Mon Sep 17 00:00:00 2001 From: jhein32 Date: Tue, 23 Aug 2016 14:44:54 +0200 Subject: [PATCH 181/701] typo fixed --- .../m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb index b24967a55e..eade0fd4f9 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [BITBUCKET_DOWNLOADS] sources = [SOURCE_TAR_GZ] -dependencies = [('Python', '2,7.12')] +dependencies = [('Python', '2.7.12')] sanity_check_paths = { 'files': [], -- GitLab From cd5f1ffe6077d1979e724bf7b2df79ae1ab6f3b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2016 15:07:33 +0200 Subject: [PATCH 182/701] extend list of X11 components, add missing deps --- .../x/X11/X11-20160819-intel-2016b.eb | 71 +++++++++++++++---- 1 file changed, 57 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb index 939b3393dd..f735807177 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -20,6 +20,10 @@ builddependencies = [ ('Autotools', '20150215'), ('pkg-config', '0.29.1'), ] +dependencies = [ + ('freetype', '2.6.5'), + ('fontconfig', '2.12.1'), +] default_easyblock = 'ConfigureMake' @@ -32,40 +36,79 @@ components = [ 'sources': ['util-macros-%(version)s.tar.gz'], 'start_dir': 'util-macros-%(version)s', }), + ('libpthread-stubs', '0.3', common_specs), + ('bigreqsproto', '1.1.2', common_specs), + ('compositeproto', '0.4.2', common_specs), + ('damageproto', '1.2.1', common_specs), + ('dmxproto', '2.3.1', common_specs), + ('dri2proto', '2.8', common_specs), + ('dri3proto', '1.0', common_specs), ('fixesproto', '5.0', common_specs), + ('fontsproto', '2.1.3', common_specs), ('glproto', '1.4.17', common_specs), - ('xextproto', '7.3.0', common_specs), - ('xcb-proto', '1.11', common_specs), ('inputproto', '2.3.1', common_specs), - ('xproto', '7.0.28', common_specs), - ('libpthread-stubs', '0.3', common_specs), ('kbproto', '1.0.7', common_specs), - ('xtrans', '1.3.5', common_specs), - ('xineramaproto', '1.2.1', common_specs), + ('presentproto', '1.0', common_specs), ('randrproto', '1.5.0', common_specs), + ('recordproto', '1.14.2', common_specs), ('renderproto', '0.11', common_specs), + ('resourceproto', '1.2.0', common_specs), + ('scrnsaverproto', '1.2.2', common_specs), + ('videoproto', '2.3.3', common_specs), + ('xcmiscproto', '1.2.2', common_specs), + ('xextproto', '7.3.0', common_specs), + ('xf86bigfontproto', '1.2.0', common_specs), + ('xf86dgaproto', '2.1', common_specs), + ('xf86driproto', '2.1.1', common_specs), + ('xf86vidmodeproto', '2.3.1', common_specs), + ('xineramaproto', '1.2.1', common_specs), + ('xproto', '7.0.28', common_specs), ('libXau', '1.0.8', common_specs), + ('libXdmcp', '1.1.2', common_specs), + ('xcb-proto', '1.11', common_specs), ('libxcb', '1.11.1', common_specs), - ('xcb-util', '0.4.0', common_specs), - ('xcb-util-image', '0.4.0', common_specs), - ('xcb-util-keysyms', '0.4.0', common_specs), - ('xcb-util-renderutil', '0.3.9', common_specs), - ('xcb-util-wm', '0.4.1', common_specs), + ('xtrans', '1.3.5', common_specs), ('libxkbcommon', '0.6.1', { 'sources': ['libxkbcommon-%(version)s.tar.xz'], 'start_dir': 'libxkbcommon-%(version)s', }), ('libX11', '1.6.3', common_specs), - ('libXrender', '0.9.9', common_specs), + ('libXext', '1.3.3', common_specs), + ('libFS', '1.0.7', common_specs), ('libICE', '1.0.9', common_specs), ('libSM', '1.2.2', common_specs), + ('libXScrnSaver', '1.2.2', common_specs), ('libXt', '1.1.5', common_specs), - ('libXext', '1.3.3', common_specs), + ('libXmu', '1.1.2', common_specs), + ('libXpm', '3.5.11', common_specs), + ('libXaw', '1.0.13', common_specs), ('libXfixes', '5.0.2', common_specs), - ('libXi', '1.7.6', common_specs), + ('libXcomposite', '0.4.4', common_specs), + ('libXrender', '0.9.9', common_specs), ('libXcursor', '1.1.14', common_specs), + ('libXdamage', '1.1.4', common_specs), + ('libfontenc', '1.1.3', common_specs), + ('libXfont', '1.5.1', common_specs), + ('libXft', '2.3.2', common_specs), + ('libXi', '1.7.6', common_specs), ('libXinerama', '1.1.3', common_specs), ('libXrandr', '1.5.0', common_specs), + ('libXres', '1.0.7', common_specs), + ('libXtst', '1.2.2', common_specs), + ('libXv', '1.0.10', common_specs), + ('libXvMC', '1.0.9', common_specs), + ('libXxf86dga', '1.1.4', common_specs), + ('libXxf86vm', '1.1.4', common_specs), + ('libdmx', '1.1.3', common_specs), + ('libpciaccess', '0.13.4', common_specs), + ('libxkbfile', '1.0.9', common_specs), + ('libxshmfence', '1.2', common_specs), + ('xcb-util', '0.4.0', common_specs), + ('xcb-util-image', '0.4.0', common_specs), + ('xcb-util-keysyms', '0.4.0', common_specs), + ('xcb-util-renderutil', '0.3.9', common_specs), + ('xcb-util-wm', '0.4.1', common_specs), + ('xcb-util-cursor', '0.1.3', common_specs), ] # Python is required for xcb-proto -- GitLab From f7715227bdba781cd2bd6562078cfeb20f2f31c2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 Aug 2016 15:22:40 +0200 Subject: [PATCH 183/701] Use github for Libint download url --- easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index f69e8361ef..c6524d3b03 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -8,8 +8,8 @@ description = """Libint library is used to evaluate the traditional (electron re toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True} -sources = [SOURCELOWER_TAR_GZ] -source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] +source_urls = ['https://github.com/evaleev/libint/archive/'] configopts = "--enable-deriv --enable-r12" -- GitLab From e8e842803cfc1afb1b4824356698cd3ea0422599 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2016 15:29:42 +0200 Subject: [PATCH 184/701] add easyconfig Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb --- ...olpro-mpp-2015.1.10.linux_x86_64_openmp.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb new file mode 100644 index 0000000000..22912ecf4a --- /dev/null +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb @@ -0,0 +1,20 @@ +name = 'Molpro' +versionprefix = 'mpp-' +version = '2015.1.10' +versionsuffix = '.linux_x86_64_openmp' + +homepage = 'https://www.molpro.net' +description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# no source URL available, requires registration to download +sources = ['%(namelower)s-%(versionprefix)s%(version)s%(versionsuffix)s.sh'] + +precompiled_binaries = True + +# license file - uncomment if a licence file is supplied by your site and +# is valid for all users - the value of license_file may have to be changed +#license_file = HOME + '/licenses/%(name)s/license.lic' + +moduleclass = 'chem' -- GitLab From 4b7a1c69ef2e444173dd51554a5f3a4be96f9b36 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2016 15:32:41 +0200 Subject: [PATCH 185/701] add easyconfig fontconfig-2.12.1-intel-2016b.eb --- .../fontconfig-2.12.1-intel-2016b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-intel-2016b.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-intel-2016b.eb new file mode 100644 index 0000000000..a2cd748981 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' + +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': '2016b'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', '2.6.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' -- GitLab From ce3efc1416bef53c0cebca7678bdba5265517fac Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 23 Aug 2016 14:34:41 +0100 Subject: [PATCH 186/701] Added comments and use %(version)s --- .../a/ABINIT/ABINIT-7.6.2-foss-2015a.eb | 14 +++++--------- .../a/ABINIT/ABINIT-7.6.2_named-constant.patch | 2 ++ .../easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch | 1 + 3 files changed, 8 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb index b50c69f2c4..35d592c177 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb @@ -4,8 +4,7 @@ name = 'ABINIT' version = '7.6.2' 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': 'foss', 'version': '2015a'} @@ -18,18 +17,15 @@ configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib64 -lnetcdf -L$EBROOTNETCD configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' configopts += '--with-trio-flavor=netcdf+etsf_io --with-dft-flavor=libxc --enable-gw-dpc' -patches = ['ABINIT-7.6.2_named-constant.patch', - 'ABINIT-7.6.2_odamix.patch', -] +patches = ['ABINIT-%(version)s_named-constant.patch', + 'ABINIT-%(version)s_odamix.patch',] dependencies = [ ('netCDF', '4.3.2'), - ('netCDF-Fortran', '4.4.0'), -] + ('netCDF-Fortran', '4.4.0'),] sanity_check_paths = { 'files': ["bin/abinit"], - 'dirs': [] -} + 'dirs': []} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch index 612de708f5..bb56a05a0a 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch @@ -1,3 +1,5 @@ +# This patch fixes a 'cannot assign to a named constant' error that occurs during the build. +# Suggested fix from: https://lists.debian.org/debian-mentors/2014/08/msg00475.html --- src/62_ctqmc/defs.h.orig 2014-02-15 21:30:20.000000000 +0000 +++ src/62_ctqmc/defs.h 2016-08-22 13:05:09.473620286 +0100 @@ -5,11 +5,11 @@ diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch index 0c5fe6dcf3..2ea83d3829 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch @@ -1,3 +1,4 @@ +# This fixes a build time error that is acknowledged here: http://forum.abinit.org/viewtopic.php?f=3&t=2656 --- src/67_common/odamix.F90.orig 2016-08-22 13:27:30.289621140 +0100 +++ src/67_common/odamix.F90 2016-08-22 13:27:40.063570238 +0100 @@ -544,7 +544,7 @@ -- GitLab From 8be4555ec687df9b6878c124678b1ed311fd9ab4 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 23 Aug 2016 14:56:34 +0100 Subject: [PATCH 187/701] Removed trailing spaces --- easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb index bfc37a6d79..132df40d05 100644 --- a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb @@ -4,7 +4,10 @@ name = 'BayPass' version = '2.1' homepage = 'http://www1.montpellier.inra.fr/CBGP/software/baypass/' -description = """The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).""" +description = """The package BayPass is a population genomics software which is primarily + aimed at identifying genetic markers subjected to selection and/or associated to + population-specific covariates (e.g., environmental variables, quantitative or + categorical phenotypic characteristics).""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'openmp': True} @@ -17,7 +20,7 @@ start_dir = 'sources' files_to_copy = [(['g_baypass'], 'bin'), (['BayPass_manual_2.1.pdf'], 'manual'), 'examples', 'utils'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/g_baypass'], 'dirs': [], -- GitLab From a53171d894c4b375f7d613c82af4cfa080006be3 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 23 Aug 2016 15:19:47 +0100 Subject: [PATCH 188/701] Corrected sanity check --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb index fb51776cb6..7ca7db6201 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -28,7 +28,7 @@ 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] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/c"], + 'dirs': ["include/openmpi"], } moduleclass = 'mpi' -- GitLab From 30d902d7a647d0d379b7713f35a704c50879644b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2016 16:46:08 +0200 Subject: [PATCH 189/701] add easyconfig PGI-16.7-GCC-5.4.0-2.26.eb, add easyconfig numactl-2.0.11-GCCcore-5.4.0.eb --- .../n/numactl/numactl-2.0.11-GCCcore-5.4.0.eb | 25 +++++++++++++++++++ .../p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..61ae200dde --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +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': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +builddependencies = [('binutils', '2.26')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..4517a84694 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '16.7' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['5594e5cab050bba07ed5f7741bc4c5e8'] + +gccver = '5.4.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' -- GitLab From a2aa57fd479695236676f38b7d55673ac301b378 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 23 Aug 2016 15:59:37 +0100 Subject: [PATCH 190/701] Removed unnecessary osdependencies --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb index 7ca7db6201..23deffc8f4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -20,10 +20,10 @@ 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'), ('libpciaccess-devel'), ('libudev-devel', 'systemd-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +# VampirTrace is no longer used : https://www.open-mpi.org/community/lists/announce/2016/07/0085.php libs = ["mpi_mpifh", "mpi", "ompitrace", "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 89aa316fafb1cadb9741f0002933b270961edac1 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 23 Aug 2016 18:46:12 -0500 Subject: [PATCH 191/701] Adding Easyconfig for VEGAS --- easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb diff --git a/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb new file mode 100644 index 0000000000..808f8cae84 --- /dev/null +++ b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'VEGAS' +version = '0.8.27' + +homepage = 'http://gump.qimr.edu.au/VEGAS/' +description = """ VEGAS (Versatile Gene-based Association Study) is +a free program for performing gene-based tests for association using +the results from genetic association studies """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://gump.qimr.edu.au/VEGAS/'] +sources = ['vegas-%(version)s-hapmapCEU.tar.gz'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["vegas", "glist-hg18", "VEGAS-readme.pdf"], + 'dirs': ["hapmapCEU"] +} + +moduleclass = 'bio' -- GitLab From 28749e68c1b55c1fb4ebd725cb8875a91bdcfa97 Mon Sep 17 00:00:00 2001 From: Ravi Tripathi Date: Tue, 23 Aug 2016 18:48:58 -0500 Subject: [PATCH 192/701] Adding checksum value --- easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb index 808f8cae84..83780a4e6c 100644 --- a/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb +++ b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://gump.qimr.edu.au/VEGAS/'] sources = ['vegas-%(version)s-hapmapCEU.tar.gz'] +checksums= ["87ca985fec0c64820bfd202f15fb31de"] + modextrapaths = {'PATH': ''} sanity_check_paths = { -- GitLab From f97dbafbb2d5eb59eb186249960f4b6518d59e25 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 09:51:04 +0200 Subject: [PATCH 193/701] Libint: generate configure script first --- easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index c6524d3b03..5a7a08275b 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -11,6 +11,10 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True} sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] +builddependencies = [('Autotools', '20150119')] + +preconfigopts = "aclocal -I lib/autoconf && autoconf && " + configopts = "--enable-deriv --enable-r12" sanity_check_paths = { -- GitLab From 040c164ec67b4984d5e0517899a8f0004f48a67f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 09:51:59 +0200 Subject: [PATCH 194/701] Use correct version for Autotools --- easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index 5a7a08275b..11e961dc88 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -11,7 +11,7 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True} sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] -builddependencies = [('Autotools', '20150119')] +builddependencies = [('Autotools', '20150215')] preconfigopts = "aclocal -I lib/autoconf && autoconf && " -- GitLab From 3f99ad4f293c641c72fd9c6972ec38c5add3cf75 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 10:03:11 +0200 Subject: [PATCH 195/701] Fix libtool version issue --- easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index 11e961dc88..d7eb544ed8 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/evaleev/libint/archive/'] builddependencies = [('Autotools', '20150215')] -preconfigopts = "aclocal -I lib/autoconf && autoconf && " +preconfigopts = "aclocal && autoconf && " configopts = "--enable-deriv --enable-r12" -- GitLab From e7b7e12c9fe4104d6b1eff98ff1d5f1fd864ef75 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 11:57:14 +0200 Subject: [PATCH 196/701] Also let libtool run --- easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index d7eb544ed8..e374aad112 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/evaleev/libint/archive/'] builddependencies = [('Autotools', '20150215')] -preconfigopts = "aclocal && autoconf && " +preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " configopts = "--enable-deriv --enable-r12" -- GitLab From 7015b6c142965dd021a13649989fb5aeae4666f7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 13:57:37 +0200 Subject: [PATCH 197/701] Add correct CP2K version --- .../c/CP2K/CP2K-3.0-intel-2016a.eb | 1 - .../c/CP2K/CP2K-3.0-intel-2016b.eb | 42 +++++++++++++++++++ 2 files changed, 42 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb index 288fa34d5e..0d4b888476 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb @@ -36,7 +36,6 @@ parallel = 1 # regression test reports failures ignore_regtest_fails = True - plumed = True moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb new file mode 100644 index 0000000000..32c292daf2 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb @@ -0,0 +1,42 @@ +name = 'CP2K' +version = '3.0' + +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': 'intel', 'version': '2016b'} +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', '1.1.6'), + ('libxc', '3.0.0'), + ('PLUMED', '2.2.3'), + ('libxsmm', '1.4.4'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# 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 + +plumed = True + +moduleclass = 'chem' -- GitLab From bd86fbd1e1dd64f6625b9a844a3ca335808cc0d0 Mon Sep 17 00:00:00 2001 From: jhein32 Date: Wed, 24 Aug 2016 14:46:40 +0200 Subject: [PATCH 198/701] Fileset for an iomkl toolchain based on icc 2013.03 and gcc 5.4 --- .../h/HPL/HPL-2.1-iomkl-2016.03b.eb | 18 +++++++++ ...11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 23 +++++++++++ .../i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb | 19 +++++++++ .../easyconfigs/i/iomkl/iomkl-2016.03b.eb | 20 ++++++++++ .../easyconfigs/i/iompi/iompi-2016.03b.eb | 19 +++++++++ ...0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 27 +++++++++++++ ...10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 39 +++++++++++++++++++ 7 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.03b.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2016.03b.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2016.03b.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.03b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.03b.eb new file mode 100644 index 0000000000..ffef7bda94 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.03b.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': 'iomkl', 'version': '2016.03b'} +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-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..b656f492fe --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +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': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} + +dependencies = [('numactl', '2.0.11')] + +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/i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb new file mode 100644 index 0000000000..b1e79f9023 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb @@ -0,0 +1,19 @@ +name = 'imkl' +version = '11.3.3.210' + +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': 'iompi', 'version': '2016.03b'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = '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/iomkl/iomkl-2016.03b.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.03b.eb new file mode 100644 index 0000000000..5d9f057934 --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.03b.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '2016.03b' + +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 = '2016.3.210-GCC-5.4.0-2.26' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('OpenMPI', '1.10.3', '', ('iccifort', compver)), + ('imkl', '11.3.3.210', '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.03b.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.03b.eb new file mode 100644 index 0000000000..7643f45613 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.03b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'iompi' +version = '2016.03b' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210-GCC-5.4.0-2.26' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('OpenMPI', '1.10.3', '', ('iccifort', compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..377f0bee91 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +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': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +# builddependencies = [('Autotools', '20150215', '', ('GCC', '5.4.0-2.26'))] + +# preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..ed7694b56f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.3' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} + +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 +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +dependencies = [('hwloc', '1.11.3')] + +# 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 libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + +moduleclass = 'mpi' -- GitLab From 075b7b45d3ac85bd685e4ef321411fb944d6dfdd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 15:42:54 +0200 Subject: [PATCH 199/701] Use libxc/2.2.3 instead of 3.0.0 --- .../c/CP2K/CP2K-3.0-intel-2016b-psmp.eb | 2 +- .../c/CP2K/CP2K-3.0-intel-2016b.eb | 2 +- .../l/libxc/libxc-2.2.3-intel-2016b.eb | 31 +++++++++++++++++++ 3 files changed, 33 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb index edc9451097..70102c177e 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb @@ -21,7 +21,7 @@ patches = [ dependencies = [ ('Libint', '1.1.6'), - ('libxc', '3.0.0'), + ('libxc', '2.2.3'), ('PLUMED', '2.2.3'), ('libxsmm', '1.4.4'), ] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb index 32c292daf2..edd1ebec09 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb @@ -20,7 +20,7 @@ patches = [ dependencies = [ ('Libint', '1.1.6'), - ('libxc', '3.0.0'), + ('libxc', '2.2.3'), ('PLUMED', '2.2.3'), ('libxsmm', '1.4.4'), ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb new file mode 100644 index 0000000000..a8378f3087 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +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': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# 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%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From cf9a3e3a16c2da74b74d87f922f3005810b59a6a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 16:31:25 +0200 Subject: [PATCH 200/701] Added OpenFOAM/4.0 --- .../b/Boost/Boost-1.61.0-intel-2016b.eb | 21 ++++++++ .../c/CGAL/CGAL-4.8.1-intel-2016b.eb | 32 ++++++++++++ .../METIS/METIS-5.1.0-intel-2016b-32bitIDX.eb | 24 +++++++++ .../o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb | 45 +++++++++++++++++ .../ParaView-5.1.0-intel-2016b-mpi.eb | 50 +++++++++++++++++++ .../easyconfigs/q/Qt/Qt-4.8.7-intel-2016b.eb | 28 +++++++++++ .../q/Qt5/Qt5-5.7.0-intel-2016b.eb | 28 +++++++++++ .../s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb | 14 ++++++ 8 files changed, 242 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b-32bitIDX.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.1.0-intel-2016b-mpi.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016b.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb new file mode 100644 index 0000000000..370bb22280 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.61.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb new file mode 100644 index 0000000000..e6a3b147ae --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb @@ -0,0 +1,32 @@ +name = 'CGAL' +version = '4.8.1' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Boost', '1.61.0'), + ('MPFR', '3.1.4'), + ('GMP', '6.1.1'), + ('libGLU', '9.0.0'), + ('Qt5', '5.7.0'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.5.2'), + ('Eigen', '3.2.9'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b-32bitIDX.eb new file mode 100644 index 0000000000..9c8e6cc340 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b-32bitIDX.eb @@ -0,0 +1,24 @@ +name = 'METIS' +version = '5.1.0' +# default 32-bit IDTYPEWIDTH, no patch used +versionsuffix = '-32bitIDX' + +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': '2016b'} +toolchainopts = {'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', +] + +builddependencies = [('CMake', '3.5.2')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb new file mode 100644 index 0000000000..811d45648a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb @@ -0,0 +1,45 @@ +name = 'OpenFOAM' +version = '4.0' + +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': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +paraversion = '5.1.0' +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-%(version)s_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir + 'OpenFOAM-%(version)s_external-3rd.patch', + ('ThirdParty-%(version)s_external-3rd.patch', ".."), + 'OpenFOAM-%%(version)s_external_paraview-%s.patch' % paraversion, +] + +dependencies = [ + ('CGAL', '4.8.1'), + ('libreadline', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0', '-32bitIDX'), + ('ncurses', '6.0'), + ('ParaView', paraversion, '-mpi'), + ('SCOTCH', '6.0.4'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.5.2'), + ('flex', '2.6.0'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.0-intel-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.0-intel-2016b-mpi.eb new file mode 100644 index 0000000000..efcf03805f --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.0-intel-2016b-mpi.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.1.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': 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"] + +# patches = ['%(name)s-%(version)s_missingheader.patch'] + +dependencies = [ + ('X11', '20160819'), + ('Mesa', '12.0.0'), + ('libGLU', '9.0.0'), + ('Qt', '4.8.7'), + ('zlib', '1.2.8'), + ('HDF5', '1.8.17'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.5.2')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.so ' +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +#configopts += '-DVTK_USE_X=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016b.eb new file mode 100644 index 0000000000..9a342ad599 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016b.eb @@ -0,0 +1,28 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016b'} + +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'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.24'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb new file mode 100644 index 0000000000..139d66073b --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.24'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb new file mode 100644 index 0000000000..20bc255b1a --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb @@ -0,0 +1,14 @@ +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': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' -- GitLab From 7a9004de176a65cac1ca7f7db0d2250393a7077a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 25 Aug 2016 10:06:19 +0200 Subject: [PATCH 201/701] Fix remarks --- easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb index 1a352ec391..56cf148c48 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb @@ -6,7 +6,7 @@ description = """Libint library is used to evaluate the traditional (electron re matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'opt': True, 'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index e374aad112..accf89b9e8 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -6,7 +6,7 @@ description = """Libint library is used to evaluate the traditional (electron re matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" toolchain = {'name': 'intel', 'version': '2016b'} -toolchainopts = {'opt': True, 'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] -- GitLab From 985e43409ce62ca318a414e34adb96d7f9f59a26 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Thu, 25 Aug 2016 11:45:14 +0200 Subject: [PATCH 202/701] Added bzip2 as a dependency of freetype. --- .../easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb | 8 ++++++-- .../easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb | 5 ++++- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb index 3111a314be..6a3974d6d7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('bzip2', '1.0.6'), + ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb index bc610c637e..17e688188c 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('bzip2', '1.0.6'), + ] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, -- GitLab From 044308f4709f70d42ddf8cbd3a27964dbf52864a Mon Sep 17 00:00:00 2001 From: Appmaint Date: Thu, 25 Aug 2016 10:56:10 +0100 Subject: [PATCH 203/701] AutoDock 4.2.5.1 with GCC 5.2.0 --- .../a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb diff --git a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb new file mode 100644 index 0000000000..18d0d12577 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb @@ -0,0 +1,24 @@ +# Currently there is not an EasyBlock to unify AutoDock and AutoGrid so this is a happy medium until then +easyblock = 'ConfigureMake' + +name = 'AutoDock' +version = '4.2.5.1' + +homepage = 'http://autodock.scripps.edu/' +description = """AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to + a receptor of known 3D structure.""" + +toolchain = {'name': 'GCC', 'version': '5.2.0'} + +sources = ['%(namelower)ssuite-%(version)s-src.tar.gz'] +source_urls = ['http://autodock.scripps.edu/downloads/previous-releases/autodock-4-2-5/tars/dist4251/'] + +start_dir = 'autodock' + +sanity_check_paths = { + 'files': ["bin/autodock4"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From a6fca44e1696af35a3af5ac92e4e3173d3fdd49f Mon Sep 17 00:00:00 2001 From: Appmaint Date: Thu, 25 Aug 2016 11:03:52 +0100 Subject: [PATCH 204/701] AutoGrid 4.2.5.1 with GCC 5.2.0 --- .../a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb diff --git a/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb new file mode 100644 index 0000000000..9658984bd8 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb @@ -0,0 +1,24 @@ +# Currently there is not an EasyBlock to unify AutoDock and AutoGrid so this is a happy medium until then +easyblock = 'ConfigureMake' + +name = 'AutoGrid' +version = '4.2.5.1' + +homepage = 'http://autodock.scripps.edu/' +description = """AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to + a receptor of known 3D structure.""" + +toolchain = {'name': 'GCC', 'version': '5.2.0'} + +sources = ['autodocksuite-%(version)s-src.tar.gz'] +source_urls = ['http://autodock.scripps.edu/downloads/previous-releases/autodock-4-2-5/tars/dist4251/'] + +start_dir = 'autogrid' + +sanity_check_paths = { + 'files': ["bin/autogrid4"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 28a0b157f2650377858a25b2dffe206a02f1611b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 25 Aug 2016 12:36:24 +0200 Subject: [PATCH 205/701] pytest added for testing --- .../p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb | 24 ++++++++++++++++++ ...yGIMLi-20160803-foss-2016a-Python-3.5.1.eb | 9 ++++--- .../pytest-3.0.1-foss-2016a-Python-3.5.1.eb | 25 +++++++++++++++++++ 3 files changed, 54 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..80574f2254 --- /dev/null +++ b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'py' +version = '1.4.31' +versionsuffix = '-Python-%(pyver)s' + +homepage = ' http://pylib.readthedocs.org/' +description = """library with cross-python path, ini-parsing, io, code, log facilities""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb index 5c868303ad..bf649cda81 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb @@ -23,15 +23,16 @@ patches = ['%(name)s-%(version)s_openblas.patch'] builddependencies = [ ('CMake', '3.4.3'), ('CastXML', '20160617'), - ('pygccxml', '20160706', '-Python-%(pyver)s'), - ('pyplusplus', '20160707', '-Python-%(pyver)s'), + ('pygccxml', '20160706', versionsuffix), + ('pyplusplus', '20160707', versionsuffix), ] dependencies = [ ('Python', '3.5.1'), - ('matplotlib', '1.5.1', '-Python-%(pyver)s'), + ('matplotlib', '1.5.1', versionsuffix), + ('pytest', '3.0.1', versionsuffix), ('Clang', '3.7.1'), - ('Boost', '1.60.0', '-Python-%(pyver)s'), + ('Boost', '1.60.0', versionsuffix), ('zlib', '1.2.8'), ('Triangle', '1.6'), ('CppUnit', '1.12.1'), diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..85ae51712a --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,25 @@ +easyblock = "PythonPackage" + +name = 'pytest' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('py', '1.4.31', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From ad654abff1f5dde01598d5e218859c3506c685f3 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Thu, 25 Aug 2016 14:36:46 +0200 Subject: [PATCH 206/701] Fixed indentation of dependencies. --- .../easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb | 6 +++--- .../easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb index 6a3974d6d7..7836f779e2 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -12,9 +12,9 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ - ('libpng', '1.6.21'), - ('bzip2', '1.0.6'), - ] + ('libpng', '1.6.21'), + ('bzip2', '1.0.6'), +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb index 17e688188c..85c186f13b 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb @@ -12,9 +12,9 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ - ('libpng', '1.6.21'), - ('bzip2', '1.0.6'), - ] + ('libpng', '1.6.21'), + ('bzip2', '1.0.6'), +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, -- GitLab From 2a41989bed6d6b2ee7c4c31f46478dfcc7bd8146 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Aug 2016 15:19:14 +0200 Subject: [PATCH 207/701] also include bzip2 as dependency for freetype in other 2.6.3 and 2.6.5 easyconfigs --- .../easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb | 5 ++++- .../easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb index 6245460dc2..d9007b7cea 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('bzip2', '1.0.6'), +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb index 63b620f14f..0263a5b031 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.24')] +dependencies = [ + ('libpng', '1.6.24'), + ('bzip2', '1.0.6'), +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, -- GitLab From 0f45abefd9e54e787ec9b2edc84366f9a2b5ad3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Aug 2016 15:27:52 +0200 Subject: [PATCH 208/701] also include zlib dep in freetype easyconfigs --- easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb | 1 + easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb | 1 + easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb | 1 + easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb index 7836f779e2..932824a17e 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -14,6 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('libpng', '1.6.21'), ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb index 85c186f13b..d267c83653 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb @@ -14,6 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('libpng', '1.6.21'), ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb index d9007b7cea..3d89e4bbb1 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb @@ -14,6 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('libpng', '1.6.21'), ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb index 0263a5b031..bf9e0cfc01 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb @@ -14,6 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('libpng', '1.6.24'), ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), ] sanity_check_paths = { -- GitLab From 1f8a41ead32230038930972e23448f3146216570 Mon Sep 17 00:00:00 2001 From: Alan Date: Thu, 25 Aug 2016 16:05:53 +0200 Subject: [PATCH 209/701] add easyconfig eudev-3.2-GCCcore-4.9.3.eb --- .../e/eudev/eudev-3.2-GCCcore-4.9.3.eb | 33 +++++++++++++++++++ .../g/gperf/gperf-3.0.4-GCCcore-4.9.3.eb | 26 +++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.2-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/e/eudev/eudev-3.2-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..82f14302a6 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.2-GCCcore-4.9.3.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.2' + +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': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('binutils', '2.25'), + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-manpages ' +runtest = '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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..b01284c106 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-GCCcore-4.9.3.eb @@ -0,0 +1,26 @@ +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From e7aeb89e67b87b7aa7764b8450847001c53cbcd0 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Thu, 25 Aug 2016 16:07:33 +0200 Subject: [PATCH 210/701] Also updated freetype 2.6.2 with zlib and bzip2 dependencies. This to brings all 2016 versions in line with each other. --- .../easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb index ce2c31a36a..60b3db5452 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, -- GitLab From 3ad67855332e181e2c5068f8a982364a09151215 Mon Sep 17 00:00:00 2001 From: Alan Date: Thu, 25 Aug 2016 16:07:43 +0200 Subject: [PATCH 211/701] add easyconfig intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb --- .../e/expat/expat-2.2.0-GCCcore-4.9.3.eb | 20 + ...tltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb | 29 + .../p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb | 886 ++++++++++++++++++ ...arser-2.44_01-GCCcore-4.9.3-Perl-5.24.0.eb | 31 + 4 files changed, 966 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-GCCcore-4.9.3-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..cb60566c9f --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-4.9.3.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.0' + +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': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +builddependencies = [ + ('binutils', '2.25'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb new file mode 100644 index 0000000000..0acb163cda --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.24.0' + +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('XML-Parser', '2.44_01', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..dc1a3cef69 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb @@ -0,0 +1,886 @@ +name = 'Perl' +version = '5.24.0' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('binutils', '2.25')] + +exts_list = [ + ('Config::General', '2.61', { + 'source_tmpl': 'Config-General-2.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.36', { + 'source_tmpl': 'Test-Harness-3.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016060801', { + 'source_tmpl': 'Regexp-Common-2016060801.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-0.026.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.05', { + 'source_tmpl': 'DateTime-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '2.00', { + 'source_tmpl': 'DateTime-TimeZone-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4218', { + 'source_tmpl': 'Module-Build-0.4218.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.24', { + 'source_tmpl': 'Try-Tiny-0.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.24', { + 'source_tmpl': 'Params-Validate-1.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.416', { + 'source_tmpl': 'List-MoreUtils-0.416.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.34', { + 'source_tmpl': 'DateTime-1.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-2.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-1.29.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-1.636.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-0.73.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('ExtUtils::MakeMaker', '7.18', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.302037', { + 'source_tmpl': 'Test-Simple-1.302037.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-0.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-3.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.71', { + 'source_tmpl': 'URI-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.44', { + 'source_tmpl': 'Text-Diff-1.44.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.029', { + 'source_tmpl': 'IO-Socket-SSL-2.029.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.04', { + 'source_tmpl': 'Test-Version-2.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '1.120', { + 'source_tmpl': 'Test-Deep-1.120.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.002004', { + 'source_tmpl': 'Moo-2.002004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.09', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.09.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-0.64.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.058', { + 'source_tmpl': 'HTTP-Tiny-0.058.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9917', { + 'source_tmpl': 'version-0.9917.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.15', { + 'source_tmpl': 'Sub-Name-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.31', { + 'source_tmpl': 'Time-Piece-1.31.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2011', { + 'source_tmpl': 'Canary-Stability-2011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.12', { + 'source_tmpl': 'AnyEvent-7.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.33', { + 'source_tmpl': 'Expect-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY/'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-3.0612.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.15', { + 'source_tmpl': 'libwww-perl-6.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.52', { + 'source_tmpl': 'GDGraph-1.52.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967013', { + 'source_tmpl': 'Parse-RecDescent-1.967013.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-1.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.37', { + 'source_tmpl': 'XML-XPath-1.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.42', { + 'source_tmpl': 'Capture-Tiny-0.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-2.000003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', 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['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.40', { + 'source_tmpl': 'Exception-Class-1.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-2.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.007', { + 'source_tmpl': 'Test-Exception-LessClever-0.007.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.45', { + 'source_tmpl': 'Scalar-List-Utils-1.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.84', { + 'source_tmpl': 'Log-Handler-0.84.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.01', { + 'source_tmpl': 'Devel-StackTrace-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1804', { + 'source_tmpl': 'Moose-2.1804.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.410', { + 'source_tmpl': 'SQL-Statement-1.410.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9160', { + 'source_tmpl': 'CPANPLUS-0.9160.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-3.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.18', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-0.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-0.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.18', { + 'source_tmpl': 'MailTools-2.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-GCCcore-4.9.3-Perl-5.24.0.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-GCCcore-4.9.3-Perl-5.24.0.eb new file mode 100644 index 0000000000..9234f03471 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-GCCcore-4.9.3-Perl-5.24.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.44_01' +versionsuffix = '-Perl-%(perlver)s' + +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25') +] + +dependencies = [ + ('Perl', '5.24.0'), + ('expat', '2.2.0') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' -- GitLab From a1aef9db0bb84d2461131607d7f0f968794cf703 Mon Sep 17 00:00:00 2001 From: Alan Date: Thu, 25 Aug 2016 16:08:59 +0200 Subject: [PATCH 212/701] add easyconfig Autotools-20150215-GCCcore-4.9.3.eb --- .../a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb | 32 +++++++++++++++++ .../a/Automake/Automake-1.15-GCCcore-4.9.3.eb | 34 +++++++++++++++++++ .../Autotools-20150215-GCCcore-4.9.3.eb | 17 ++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb | 23 +++++++++++++ 4 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..8b7fb4793d --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb @@ -0,0 +1,32 @@ +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25') +] + +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..5927ea856a --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb @@ -0,0 +1,34 @@ +## +# 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': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('binutils', '2.25')] +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..14abf09d3b --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.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': 'GCCcore', 'version': '4.9.3'} + +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..ae9366cdfd --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb @@ -0,0 +1,23 @@ +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': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('binutils', '2.25') +] + +dependencies = [ + ('M4', '1.4.17'), +] + +moduleclass = 'lib' -- GitLab From 35aa01a7c1a8bc9b6812d46c38a0bda278a0f5f4 Mon Sep 17 00:00:00 2001 From: Alan Date: Thu, 25 Aug 2016 16:12:36 +0200 Subject: [PATCH 213/701] add easyconfig freetype-2.6.5-GCCcore-4.9.3.eb --- .../freetype/freetype-2.6.5-GCCcore-4.9.3.eb | 30 +++++++++++++++++ .../l/libpng/libpng-1.6.24-GCCcore-4.9.3.eb | 32 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..e9c138419b --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb @@ -0,0 +1,30 @@ +name = 'freetype' +version = '2.6.5' + +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('libpng', '1.6.24'), +] + +configopts = '--with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..a2901e0890 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-4.9.3.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.24' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' -- GitLab From ee2aa40b6bfd69c268aeb52ade2f5c77efe888de Mon Sep 17 00:00:00 2001 From: Alan Date: Thu, 25 Aug 2016 16:14:36 +0200 Subject: [PATCH 214/701] add easyconfig LLVM-3.8.1-GCCcore-4.9.3.eb --- .../c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb | 35 ++++++++++++++++ .../l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb | 40 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..d5ca429e05 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('ncurses', '6.0'), + # 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', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..3fc9b2d6f5 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.1' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('binutils', '2.25'), + ('CMake', '3.6.1'), + # We use the system Python in GCCcore + #('Python', '2.7.12'), +] + +# We use the system Python in GCCcore +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From 04f28747560abed2082d785dc30e83f2954e4956 Mon Sep 17 00:00:00 2001 From: Alan Date: Thu, 25 Aug 2016 16:16:03 +0200 Subject: [PATCH 215/701] add easyconfig gettext-0.19.8-GCCcore-4.9.3.eb --- .../g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb | 26 +++++++++++++ .../l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb | 37 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..cd97e3e99f --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8' + +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': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +dependencies = [ + ('libxml2', '2.9.4'), +] + +builddependencies = [ + ('binutils', '2.25'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..96e7f21c7d --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.4' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +modextrapaths = {'CPATH': ['include/libxml2']} + +moduleclass = 'lib' -- GitLab From c5f38c1068f86372e7cf41cc12c74da2c3677a43 Mon Sep 17 00:00:00 2001 From: Alan Date: Thu, 25 Aug 2016 16:18:38 +0200 Subject: [PATCH 216/701] add easyconfig jhbuild-3.15.92-GCCcore-4.9.3.eb --- .../jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..ae050d4ada --- /dev/null +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'jhbuild' +version = '3.15.92' + +homepage = 'https://wiki.gnome.org/action/show/Projects/Jhbuild' +description = """JHBuild allows you to automatically download and compile “modules” (i.e. source code packages). +Modules are listed in “module set” files, which also include dependency information so that JHBuild can discover +what modules need to be built and in what order.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = ['%(version)s.tar.gz'] +source_urls = [('https://github.com/GNOME/jhbuild/archive/')] + +# jhbuild is a python script so it has a python dependency. +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +builddependencies = [ + ('binutils', '2.25') +] + +buildininstalldir=True +skipsteps = ['configure'] +prebuildopts = './autogen.sh --prefix=%(installdir)s &&' + +sanity_check_paths = { + 'files': ['bin/jhbuild'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From f58b5f072eedf1a071dce5a289ae0f61f2e719e0 Mon Sep 17 00:00:00 2001 From: Alan Date: Thu, 25 Aug 2016 16:19:38 +0200 Subject: [PATCH 217/701] add easyconfig pkg-config-0.29.1-GCCcore-4.9.3.eb --- .../pkg-config-0.29.1-GCCcore-4.9.3.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..08db3ee5e8 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +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).""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +builddependencies = [('binutils', '2.25')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From d97ba463057a6080b243738f28ed554a6800ea44 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 25 Aug 2016 16:51:14 +0200 Subject: [PATCH 218/701] perl version removed from name, perl dep to builddeps --- ..._92-Perl-5.22.1.eb => PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PLAST/{PLAST-2.3.1-foss-2016a-Java-1.8.0_92-Perl-5.22.1.eb => PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb} (100%) diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb similarity index 100% rename from easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92-Perl-5.22.1.eb rename to easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb -- GitLab From 586cefabcaa30678fff12bd2478eab6abad32d90 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 25 Aug 2016 16:55:01 +0200 Subject: [PATCH 219/701] also removed Perl in the versionsuffixline --- .../p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb index 290a7183f9..fe19e3f15f 100644 --- a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb @@ -2,7 +2,7 @@ easyblock = 'CMakeMake' name = 'PLAST' version = '2.3.1' -versionsuffix = '-Java-%(javaver)s-Perl-%(perlver)s' +versionsuffix = '-Java-%(javaver)s' homepage = "http://www.irisa.fr/symbiose/projects/plast/" description = """PLAST is a parallel alignment search tool for comparing large protein banks""" @@ -14,11 +14,11 @@ sources=['%(namelower)s_source_v%(version)s.tar.gz'] builddependencies = [ ('CMake', '3.5.2') + ('Perl', '5.22.1') ] dependencies = [ ('Java', '1.8.0_92', '', True), - ('Perl', '5.22.1') ] sanity_check_paths = { -- GitLab From 9c90b5ba9a983015187a1785d6f77ed0f6724c4d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 25 Aug 2016 16:56:49 +0200 Subject: [PATCH 220/701] style fix --- .../easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb index fe19e3f15f..f8008023a2 100644 --- a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb @@ -14,7 +14,7 @@ sources=['%(namelower)s_source_v%(version)s.tar.gz'] builddependencies = [ ('CMake', '3.5.2') - ('Perl', '5.22.1') + ('Perl', '5.22.1') ] dependencies = [ -- GitLab From 47ac34d85f094a90397d2d34b0d7b9d4cbb442e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Aug 2016 17:42:06 +0200 Subject: [PATCH 221/701] add easyconfig R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb --- ...le-Bioconductor-3.3-intel-2016b-R-3.3.1.eb | 160 ++++++++++++++++++ 1 file changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000..fdefc2a8bc --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb @@ -0,0 +1,160 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('R', '3.3.1'), + ('HDF5', '1.8.17'), # for rhdf5 +] + +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://bioconductor.org/packages/3.3/bioc/src/contrib/', + 'http://bioconductor.org/packages/3.3/data/annotation/src/contrib/', + 'http://bioconductor.org/packages/3.3/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +# 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', '0.18.0', bioconductor_options), + ('Biobase', '2.32.0', bioconductor_options), + ('S4Vectors', '0.10.3', bioconductor_options), + ('IRanges', '2.6.1', bioconductor_options), + ('GenomeInfoDb', '1.8.3', bioconductor_options), + ('AnnotationDbi', '1.34.4', bioconductor_options), + ('zlibbioc', '1.18.0', bioconductor_options), + ('XVector', '0.12.1', bioconductor_options), + ('Biostrings', '2.40.2', bioconductor_options), + ('GenomicRanges', '1.24.2', bioconductor_options), + ('BiocParallel', '1.6.6', bioconductor_options), + ('Rsamtools', '1.24.0', bioconductor_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('SummarizedExperiment', '1.2.3', bioconductor_options), + ('GenomicAlignments', '1.8.4', bioconductor_options), + ('ShortRead', '1.30.0', bioconductor_options), + ('graph', '1.50.0', bioconductor_options), + ('affyio', '1.42.0', bioconductor_options), + ('BiocInstaller', '1.22.3', bioconductor_options), + ('preprocessCore', '1.34.0', bioconductor_options), + ('affy', '1.50.0', bioconductor_options), + ('GO.db', '3.3.0', bioconductor_options), + ('limma', '3.28.19', bioconductor_options), + ('RBGL', '1.48.1', bioconductor_options), + ('org.Hs.eg.db', '3.3.0', bioconductor_options), + ('AnnotationForge', '1.14.2', bioconductor_options), + ('KEGG.db', '3.2.3', bioconductor_options), + ('annaffy', '1.44.0', bioconductor_options), + ('gcrma', '2.44.0', bioconductor_options), + ('oligoClasses', '1.34.0', bioconductor_options), + ('edgeR', '3.14.0', bioconductor_options), + ('PFAM.db', '3.3.0', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.6.0', bioconductor_options), + ('qvalue', '2.4.2', bioconductor_options), + ('impute', '1.46.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.26.0', bioconductor_options), + ('hgu133plus2.db', '3.2.3', bioconductor_options), + ('illuminaio', '0.14.0', bioconductor_options), + ('rtracklayer', '1.32.2', bioconductor_options), + ('biomaRt', '2.28.0', bioconductor_options), + ('GenomicFeatures', '1.24.5', bioconductor_options), + ('bumphunter', '1.12.0', bioconductor_options), + ('multtest', '2.28.0', bioconductor_options), + ('siggenes', '1.46.0', bioconductor_options), + ('DynDoc', '1.50.0', bioconductor_options), + ('genoset', '1.28.2', bioconductor_options), + ('NOISeq', '2.16.0', bioconductor_options), + ('Rgraphviz', '2.16.0', bioconductor_options), + ('RNASeqPower', '1.12.0', bioconductor_options), + ('annotate', '1.50.0', bioconductor_options), + ('GSEABase', '1.34.0', bioconductor_options), + ('genefilter', '1.54.2', bioconductor_options), + ('Category', '2.38.0', bioconductor_options), + ('GOstats', '2.38.1', bioconductor_options), + ('BSgenome', '1.40.1', bioconductor_options), + ('VariantAnnotation', '1.18.7', bioconductor_options), + ('interactiveDisplayBase', '1.10.3', bioconductor_options), + ('AnnotationHub', '2.4.2', bioconductor_options), + ('ensembldb', '1.4.7', bioconductor_options), + ('biovizBase', '1.20.0', bioconductor_options), + ('OrganismDbi', '1.14.1', bioconductor_options), + ('ggbio', '1.20.2', bioconductor_options), + ('geneplotter', '1.50.0', bioconductor_options), + ('DESeq2', '1.12.4', bioconductor_options), + ('ReportingTools', '2.12.2', bioconductor_options), + ('affycoretools', '1.44.3', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', bioconductor_options), + ('Homo.sapiens', '1.3.1', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.22.0', bioconductor_options), + ('GenomeGraphs', '1.32.0', bioconductor_options), + ('geneLenDataBase', '1.8.0', bioconductor_options), + ('goseq', '1.24.0', bioconductor_options), + ('KEGGREST', '1.12.2', bioconductor_options), + ('KEGGgraph', '1.30.0', bioconductor_options), + ('KEGGprofile', '1.14.0', bioconductor_options), + ('GEOquery', '2.38.4', bioconductor_options), + ('mixOmics', '6.0.0', ext_options), + ('minfi', '1.18.6', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.18.2', bioconductor_options), + ('lumi', '2.24.0', bioconductor_options), + ('widgetTools', '1.50.0', bioconductor_options), + ('tkWidgets', '1.50.0', bioconductor_options), + ('Mfuzz', '2.32.0', bioconductor_options), + ('maSigPro', '1.44.0', bioconductor_options), + ('SPIA', '2.24.0', bioconductor_options), + ('Gviz', '1.16.4', bioconductor_options), + ('cummeRbund', '2.14.0', bioconductor_options), + ('GenomicFiles', '1.8.0', bioconductor_options), + ('derfinderHelper', '1.6.3', bioconductor_options), + ('derfinder', '1.6.4', bioconductor_options), + ('polyester', '1.8.3', bioconductor_options), + ('Rsubread', '1.22.3', bioconductor_options), + ('pcaMethods', '1.64.0', bioconductor_options), + ('marray', '1.50.0', bioconductor_options), + ('CGHbase', '1.32.0', bioconductor_options), + ('sigaR', '1.15.0', bioconductor_options), + ('HCsnip', '1.12.0', bioconductor_options), + ('metagenomeSeq', '1.14.2', bioconductor_options), + ('gdsfmt', '1.8.3', bioconductor_options), + ('rhdf5', '2.16.0', bioconductor_options), + ('biomformat', '1.0.2', bioconductor_options), + ('phyloseq', '1.16.2', bioconductor_options), + ('ALDEx2', '1.4.0', bioconductor_options), + ('dada2', '1.0.3', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From baeede5d11667d8851a32cc3f5eec0549c625cf0 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Thu, 25 Aug 2016 16:44:30 +0100 Subject: [PATCH 222/701] Fixed style issue --- .../easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb index 18d0d12577..58598fa8b4 100644 --- a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb @@ -5,8 +5,8 @@ name = 'AutoDock' version = '4.2.5.1' homepage = 'http://autodock.scripps.edu/' -description = """AutoDock is a suite of automated docking tools. It is designed to - predict how small molecules, such as substrates or drug candidates, bind to +description = """AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.""" toolchain = {'name': 'GCC', 'version': '5.2.0'} @@ -17,8 +17,8 @@ source_urls = ['http://autodock.scripps.edu/downloads/previous-releases/autodock start_dir = 'autodock' sanity_check_paths = { - 'files': ["bin/autodock4"], - 'dirs': [] + 'files': ["bin/autodock4"], + 'dirs': [] } moduleclass = 'tools' -- GitLab From 2885a7d71bd61c8b988a809a87aa1a89ae1dc2b0 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Thu, 25 Aug 2016 16:46:34 +0100 Subject: [PATCH 223/701] Fixed style issue --- .../easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb index 9658984bd8..1cb41f8b79 100644 --- a/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb @@ -5,8 +5,8 @@ name = 'AutoGrid' version = '4.2.5.1' homepage = 'http://autodock.scripps.edu/' -description = """AutoDock is a suite of automated docking tools. It is designed to - predict how small molecules, such as substrates or drug candidates, bind to +description = """AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.""" toolchain = {'name': 'GCC', 'version': '5.2.0'} @@ -17,8 +17,8 @@ source_urls = ['http://autodock.scripps.edu/downloads/previous-releases/autodock start_dir = 'autogrid' sanity_check_paths = { - 'files': ["bin/autogrid4"], - 'dirs': [] + 'files': ["bin/autogrid4"], + 'dirs': [] } moduleclass = 'tools' -- GitLab From 8c0a97908de1ef5e45ffb908d5756588f0aef4c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Aug 2016 20:04:50 +0200 Subject: [PATCH 224/701] fix minor style issues (indent/order/long lines) --- .../a/ABINIT/ABINIT-7.6.2-foss-2015a.eb | 23 +++++++++++-------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb index 35d592c177..bfa5f0befa 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb @@ -4,28 +4,33 @@ name = 'ABINIT' version = '7.6.2' 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': 'foss', 'version': '2015a'} source_urls = ['http://ftp.abinit.org/'] sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'ABINIT-%(version)s_named-constant.patch', + 'ABINIT-%(version)s_odamix.patch', +] + +dependencies = [ + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + configopts = '--enable-mpi --with-mpi-prefix="$EBROOTOPENMPI" --enable-fallbacks ' configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib64 -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' configopts += '--with-trio-flavor=netcdf+etsf_io --with-dft-flavor=libxc --enable-gw-dpc' -patches = ['ABINIT-%(version)s_named-constant.patch', - 'ABINIT-%(version)s_odamix.patch',] - -dependencies = [ - ('netCDF', '4.3.2'), - ('netCDF-Fortran', '4.4.0'),] - sanity_check_paths = { 'files': ["bin/abinit"], - 'dirs': []} + 'dirs': [], +} moduleclass = 'chem' -- GitLab From 9fdd04cad8198e95e4741e67a7f9d491b623ba4a Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 26 Aug 2016 09:07:12 +0200 Subject: [PATCH 225/701] add easyconfig freetype-2.6.5-GCCcore-4.9.3.eb --- .../b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb | 19 +++++++++++++++++++ .../freetype/freetype-2.6.5-GCCcore-4.9.3.eb | 2 ++ 2 files changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..3f3812483e --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb @@ -0,0 +1,19 @@ +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': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +builddependencies = [ + ('binutils', '2.25'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb index e9c138419b..2c7c4b34ee 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb @@ -17,6 +17,8 @@ builddependencies = [ dependencies = [ ('libpng', '1.6.24'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), ] configopts = '--with-harfbuzz=no' -- GitLab From 388ab1afec8ec8647d11440292dcde6d6b84fa25 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 26 Aug 2016 09:10:28 +0200 Subject: [PATCH 226/701] add easyconfig gettext-0.19.8-GCCcore-4.9.3.eb --- .../g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb index cd97e3e99f..8e1b03ad2a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb @@ -13,14 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' +builddependencies = [ + ('binutils', '2.25'), +] dependencies = [ ('libxml2', '2.9.4'), + ('ncurses', '6.0'), ] -builddependencies = [ - ('binutils', '2.25'), -] +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' moduleclass = 'vis' -- GitLab From 60b0f8927afc57f74a0678442c57aac515fc48be Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 26 Aug 2016 09:10:34 +0200 Subject: [PATCH 227/701] missing comma --- .../easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb index f8008023a2..bb22d3db40 100644 --- a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/PLAST-software/plast-library/releases/downloa sources=['%(namelower)s_source_v%(version)s.tar.gz'] builddependencies = [ - ('CMake', '3.5.2') + ('CMake', '3.5.2'), ('Perl', '5.22.1') ] -- GitLab From 7a0f2e5deab64e21b5423e73c59990beeb2bbab6 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 26 Aug 2016 09:58:48 +0200 Subject: [PATCH 228/701] strict var on True --- .../o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb index a511a38eb3..5289372a0b 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """Open Babel is a chemical toolbox designed to speak the many solid-state materials, biochemistry, or related areas.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True} +toolchainopts = {'optarch': True, 'strict': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 71b9468f83b4b3dd34a2de84e995c9803e09908e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2016 10:06:14 +0200 Subject: [PATCH 229/701] add SNPRelate along with required patch --- .../R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb index fdefc2a8bc..c43e3ff869 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb @@ -143,6 +143,7 @@ exts_list = [ ('HCsnip', '1.12.0', bioconductor_options), ('metagenomeSeq', '1.14.2', bioconductor_options), ('gdsfmt', '1.8.3', bioconductor_options), + ('SNPRelate', '1.6.5', dict(bioconductor_options.items() + [('patches', ['SNPRelate-1.6.5_no-SSE-intr.patch'])])), ('rhdf5', '2.16.0', bioconductor_options), ('biomformat', '1.0.2', bioconductor_options), ('phyloseq', '1.16.2', bioconductor_options), -- GitLab From 28bf6806536bc93aa4d1353f21e15c2658271e87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2016 10:09:45 +0200 Subject: [PATCH 230/701] add missing patch file for SNPRelate --- .../SNPRelate-1.6.5_no-SSE-intr.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/SNPRelate-1.6.5_no-SSE-intr.patch diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/SNPRelate-1.6.5_no-SSE-intr.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/SNPRelate-1.6.5_no-SSE-intr.patch new file mode 100644 index 0000000000..cb934b50ee --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/SNPRelate-1.6.5_no-SSE-intr.patch @@ -0,0 +1,15 @@ +disable SSE intrinsics to avoid error when compiling with Intel C++ compiler: +"error: expression must have integral or enum type" +in genIBS.cpp and genKING.cpp due to use of complement (~) on values of type _m128i +author: Kenneth Hoste; patch suggested by Xiuwen Zheng (SNPRelate maintainer) +--- SNPRelate.orig/src/Makevars 2016-07-29 06:39:00.000000000 +0200 ++++ SNPRelate/src/Makevars 2016-08-26 09:31:44.440787000 +0200 +@@ -3,7 +3,7 @@ + ### ### + + # additional preprocessor options +-PKG_CPPFLAGS = -DUSING_R -I. ++PKG_CPPFLAGS = -DUSING_R -I. -DCOREARRAY_NO_SIMD + + # to set flags for the linker + PKG_LIBS = $(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS) -lpthread -- GitLab From 973c316267149e389017b60b5af02b86fea53047 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2016 10:58:18 +0200 Subject: [PATCH 231/701] add 'include/libxml2' to CPATH in libxml2 recent easyconfigs --- .../easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb | 2 ++ easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb | 2 ++ easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb | 2 ++ easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb | 2 ++ easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb | 2 ++ easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb | 2 ++ easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb | 2 ++ easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb | 2 ++ easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb | 2 ++ easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb | 2 ++ 10 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb index e7c2739dac..322d4dbeda 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb @@ -27,4 +27,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb index ba6d0a4c3f..9e15ece882 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb @@ -25,4 +25,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb index 59e0331739..ad525d1e63 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -22,4 +22,6 @@ dependencies = [ ('zlib', '1.2.8'), ] +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb index 9f21eb1b66..ed32688bef 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb index 1f39ac3f7d..cd5c7d2c15 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb index 66513c188b..d7a623361a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb index b762d96901..d29bab77ba 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb index eb799f0921..b6ee64dbb7 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb index 38d9c7eb2e..d1806d2536 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb index 9f8ee962cf..01feb5f8e8 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' -- GitLab From 3f117bd59cd96e26b20bb2b748c6d1224d235c70 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Fri, 26 Aug 2016 10:12:38 +0100 Subject: [PATCH 232/701] Boost 1.52.0 with foss 2015a --- .../b/Boost/Boost-1.52.0-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.52.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.52.0-foss-2015a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.52.0-foss-2015a.eb new file mode 100644 index 0000000000..68ec736672 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.52.0-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.52.0' + +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('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From d817e80e61c0c3d8c8d1a39dd351502ba5934108 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 26 Aug 2016 12:14:48 +0200 Subject: [PATCH 233/701] add easyconfig LLVM-3.8.1-GCCcore-4.9.3.eb --- .../l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb | 7 +-- .../Python-2.7.12-GCCcore-4.9.3-bare.eb | 31 +++++++++++++ .../s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb | 44 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb | 29 ++++++++++++ 4 files changed, 106 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb index 3fc9b2d6f5..ab5263c53f 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb @@ -20,13 +20,10 @@ sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ ('binutils', '2.25'), ('CMake', '3.6.1'), - # We use the system Python in GCCcore - #('Python', '2.7.12'), + # We use the minimal Python in GCCcore + ('Python', '2.7.12', '-bare'), ] -# We use the system Python in GCCcore -allow_system_deps = [('Python', SYS_PYTHON_VERSION)] - dependencies = [ ('ncurses', '6.0'), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb new file mode 100644 index 0000000000..c964fa0788 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.12' +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': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.14.1'), + # ('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')] + +# We hide this by default since users should not use it in production +hidden = True + +# bare installation: only known module deps for GCCcore tools included +exts_list =[] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..d38cf61101 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb @@ -0,0 +1,44 @@ +## +# 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 = '3.14.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2016/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..35b772ac6f --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 34b184b075a91c78b731f39d93f71c5fce8eeade Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 26 Aug 2016 12:21:16 +0200 Subject: [PATCH 234/701] add easyconfig jhbuild-3.15.92-GCCcore-4.9.3.eb --- .../a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb | 32 ++++++++++++++ .../a/Automake/Automake-1.15-GCCcore-4.9.3.eb | 34 ++++++++++++++ .../Autotools-20150215-GCCcore-4.9.3.eb | 17 +++++++ .../g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb | 26 +++++++++++ .../jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 26 ++++++++--- .../l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb | 23 ++++++++++ .../l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb | 37 ++++++++++++++++ .../Python-2.7.12-GCCcore-4.9.3-bare.eb | 31 +++++++++++++ .../pkg-config-0.29.1-GCCcore-4.9.3.eb | 29 ++++++++++++ .../s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb | 44 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb | 29 ++++++++++++ 11 files changed, 322 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..8b7fb4793d --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb @@ -0,0 +1,32 @@ +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25') +] + +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..5927ea856a --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb @@ -0,0 +1,34 @@ +## +# 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': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('binutils', '2.25')] +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..14abf09d3b --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.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': 'GCCcore', 'version': '4.9.3'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..cd97e3e99f --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8' + +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': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +dependencies = [ + ('libxml2', '2.9.4'), +] + +builddependencies = [ + ('binutils', '2.25'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb index ae050d4ada..6cafa8acd8 100644 --- a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -13,18 +13,32 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} sources = ['%(version)s.tar.gz'] source_urls = [('https://github.com/GNOME/jhbuild/archive/')] -# jhbuild is a python script so it has a python dependency. -# allow use of system Python -allow_system_deps = [('Python', SYS_PYTHON_VERSION)] - +# jhbuild is python so it has a python dependency, but we want to give people freedom to use whatever python they +# chose during a build process builddependencies = [ - ('binutils', '2.25') + ('Python', '2.7.12', '-bare'), +] + +dependencies = [ + ('binutils', '2.25'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('gettext', '0.19.8'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('M4', '1.4.17'), ] -buildininstalldir=True +# We use the simple install method as per: +# https://developer.gnome.org/jhbuild/stable/getting-started.html.en +# to avoid unnecessary dependencies. This requires us to build in the install dir so that all libs are found. +buildininstalldir = True skipsteps = ['configure'] prebuildopts = './autogen.sh --prefix=%(installdir)s &&' +# Make sure there are no "not found" in the sanitycheck output +sanity_check_commands = [('! jhbuild', 'sanitycheck| grep not\ found')] + sanity_check_paths = { 'files': ['bin/jhbuild'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..ae9366cdfd --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb @@ -0,0 +1,23 @@ +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': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('binutils', '2.25') +] + +dependencies = [ + ('M4', '1.4.17'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..96e7f21c7d --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.4' + +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': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +modextrapaths = {'CPATH': ['include/libxml2']} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb new file mode 100644 index 0000000000..c964fa0788 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.12' +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': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.14.1'), + # ('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')] + +# We hide this by default since users should not use it in production +hidden = True + +# bare installation: only known module deps for GCCcore tools included +exts_list =[] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..08db3ee5e8 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +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).""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +builddependencies = [('binutils', '2.25')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..d38cf61101 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb @@ -0,0 +1,44 @@ +## +# 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 = '3.14.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2016/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..35b772ac6f --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 75f0cd702ced8c85e0b11b7500ed20caa6b7f6b2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 26 Aug 2016 13:06:01 +0200 Subject: [PATCH 235/701] use BLAST instead of BLAST+ --- .../p/{pftools => pftoolsV3}/pftoolsV3-20160324-foss-2016a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/{pftools => pftoolsV3}/pftoolsV3-20160324-foss-2016a.eb (100%) diff --git a/easybuild/easyconfigs/p/pftools/pftoolsV3-20160324-foss-2016a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb similarity index 100% rename from easybuild/easyconfigs/p/pftools/pftoolsV3-20160324-foss-2016a.eb rename to easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb -- GitLab From 7e0418a7c698fbe79e01465484c6fa3508911794 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2016 13:07:13 +0200 Subject: [PATCH 236/701] add easyconfig libcpuset-1.0.eb, add easyconfig libbitmask-2.0.eb --- .../l/libbitmask/libbitmask-2.0.eb | 23 ++++++++++++++++++ .../easyconfigs/l/libcpuset/libcpuset-1.0.eb | 24 +++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb create mode 100644 easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb diff --git a/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb b/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb new file mode 100644 index 0000000000..97242082aa --- /dev/null +++ b/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libbitmask' +version = '2.0' + +homepage = 'http://oss.sgi.com/projects/cpusets/' +description = "libbitmask provides a convenient, powerful bitmask data type" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['ftp://oss.sgi.com/projects/cpusets/download/'] +sources = [SOURCE_TAR_BZ2] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "libtoolize && aclocal && automake --add-missing && autoconf && " + +sanity_check_paths = { + 'files': ['include/bitmask.h', 'lib/libbitmask.a', 'lib/libbitmask.so'], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb b/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb new file mode 100644 index 0000000000..7f3929821a --- /dev/null +++ b/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libcpuset' +version = '1.0' + +homepage = 'http://oss.sgi.com/projects/cpusets/' +description = "libcpuset provides full access to cpuset capabilities" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['ftp://oss.sgi.com/projects/cpusets/download/'] +sources = [SOURCE_TAR_BZ2] + +builddependencies = [('Autotools', '20150215')] +dependencies = [('libbitmask', '2.0')] + +preconfigopts = "libtoolize && aclocal && mv configure.in configure.ac && automake --add-missing && autoconf && " + +sanity_check_paths = { + 'files': ['include/cpuset.h', 'lib/libcpuset.a', 'lib/libcpuset.so'], + 'dirs': ['share'], +} + +moduleclass = 'lib' -- GitLab From a4ce5801e84bdf81a7fc0386ddb3f533eff548c1 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 26 Aug 2016 13:07:33 +0200 Subject: [PATCH 237/701] use BLAST instead of BLAST+ --- .../easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index ac9f122387..9a447b3dd9 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -18,7 +18,7 @@ dependencies = [ ('Perl', '5.22.1'), ('libpsortb','1.0'), ('BioPerl','1.6.924','-Perl-5.22.1'), - ('BLAST+','2.3.0', '-Python-2.7.11'), + ('BLAST','2.2.26', '-Linux_x86_64', True), ('pftoolsV3','20160324'), ] -- GitLab From 712f5d40b96a1d112ab783f73b967bfe11be7467 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 26 Aug 2016 13:21:03 +0200 Subject: [PATCH 238/701] {geo}[foss-2016a] pyGIMLi - Python 3.5.1 (REVIEW) --- .../py/py-1.4.31-foss-2016a-Python-2.7.11.eb | 24 +++++++ ...GIMLi-20160803-foss-2016a-Python-2.7.11.eb | 68 +++++++++++++++++++ ...ccxml-20160706-foss-2016a-Python-2.7.11.eb | 32 +++++++++ ...splus-20160707-foss-2016a-Python-2.7.11.eb | 35 ++++++++++ .../pytest-3.0.1-foss-2016a-Python-2.7.11.eb | 25 +++++++ 5 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..7bd9dcc8b8 --- /dev/null +++ b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'py' +version = '1.4.31' +versionsuffix = '-Python-%(pyver)s' + +homepage = ' http://pylib.readthedocs.org/' +description = """library with cross-python path, ini-parsing, io, code, log facilities""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..908370bc3a --- /dev/null +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,68 @@ +easyblock = 'CMakeMake' + +name = 'pyGIMLi' +version = '20160803' +commit_id = 'a190c53' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pygimli.org/' +description = """pyGIMLi is an open-source multi-method library for solving inverse + and forward tasks related to geophysical problems. Written in C++ and Python, + it offers both efficiency and flexibility allowing you to quickly build + your own robust inversion applications for the geophysical problem at hand.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/gimli-org/gimli/archive/'] +sources = ['%s.tar.gz' % commit_id] + +patches = ['%(name)s-%(version)s_openblas.patch'] + +#pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus +#Check scripts/buildThirdParty.sh +builddependencies = [ + ('CMake', '3.4.3'), + ('CastXML', '20160617'), + ('pygccxml', '20160706', versionsuffix), + ('pyplusplus', '20160707', versionsuffix), +] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), + ('pytest', '3.0.1', versionsuffix), + ('Clang', '3.7.1'), + ('Boost', '1.60.0', versionsuffix), + ('zlib', '1.2.8'), + ('Triangle', '1.6'), + ('CppUnit', '1.12.1'), + ('SuiteSparse', '4.5.3', '-METIS-5.1.0'), +] + +separate_build_dir = True + +configopts = '-DBOOST_ROOT=$EBROOTBOOST ' +configopts += '-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT +configopts += '-DCASTXML_EXECUTABLE=$EBROOTCASTXML/bin/castxml ' +configopts += '-DPYGCCXML_PATH=$EBROOTPYGCCXML/lib/python%(pyshortver)s/site-packages/ ' +configopts += '-DPYPLUSPLUS_PATH=$EBROOTPYPLUSPLUS/lib/python%(pyshortver)s/site-packages/ ' + +buildopts = 'gimli pygimli apps' + +installopts = ' && mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages ' +installopts += '&& cp -a ../gimli*/python/. %(installdir)s/lib/python%(pyshortver)s/site-packages ' +installopts += '&& mkdir %(installdir)s/bin ' +installopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bms2vtk', 'dc1dinv', 'dc1dsmooth', 'fdem1dinv', 'fdem1dsmooth', + 'harmfit', 'invlinearmat', 'mrs1dblock', 'mrs1dsmooth', + 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']]+ + ['lib/libgimli.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/pygimli.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..9f63786f27 --- /dev/null +++ b/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pygccxml' +version = '20160706' +commit_id = '648e8da' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pygccxml' +description = """Python package for easy C++ declarations navigation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/gccxml/pygccxml/archive/'] +sources = ['%s.tar.gz' % commit_id] + +builddependencies = [('pip', '8.1.2', versionsuffix)] + +dependencies = [ + ('Python', '2.7.11'), + ('CastXML', '20160617'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..695617390c --- /dev/null +++ b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'pyplusplus' +version = '20160707' +commit_id = '2c6c05b7a7d2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/ompl/pyplusplus' +description = """Py++ is a code generator for Boost.Python that simplifies + writing Python bindings of a C/C++ library + The tool is implemented as a Python module which is controlled by a user script.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/ompl/pyplusplus/get/'] +sources = ['%s.zip' % commit_id] + +builddependencies = [('pip', '8.1.2', versionsuffix)] + +dependencies = [ + ('Python', '2.7.11'), + ('pygccxml', '20160706', '-Python-%(pyver)s'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a816b7e71e --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = "PythonPackage" + +name = 'pytest' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('py', '1.4.31', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From b489894cd940658471cc2264c7d58270058c4b41 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 26 Aug 2016 13:22:39 +0200 Subject: [PATCH 239/701] sync with develop --- .../easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb deleted file mode 100644 index 99e9f6bd51..0000000000 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb +++ /dev/null @@ -1,13 +0,0 @@ -name = 'Eigen' -version = '3.2.8' - -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': '2016a'} - -source_urls = [BITBUCKET_SOURCE] -sources = ['%(version)s.tar.bz2'] - -moduleclass = 'math' -- GitLab From da98bc4f92c881cfc9410c4dbfbb5b6a0b043b5b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 26 Aug 2016 13:59:23 +0200 Subject: [PATCH 240/701] change sourceforge url and provide correct sanity check --- easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb index 1613e1f3c8..03cdf3c1c3 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb @@ -12,13 +12,13 @@ description = """ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = [SOURCEFORGE_SOURCE] +source_urls = ['http://download.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic --disable-cpp --enable-jit" sanity_check_paths = { - 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "libpcre2-8.a"], + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a"], 'dirs': [], } -- GitLab From 54d6f7b271ca1fd1282b87437f26cb7b0ed7502f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2016 14:37:41 +0200 Subject: [PATCH 241/701] add easyconfig libbitmask-2.0.eb, add easyconfig libcpuset-1.0.eb --- easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb | 2 +- easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb b/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb index 97242082aa..5a0206f950 100644 --- a/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb +++ b/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_BZ2] builddependencies = [('Autotools', '20150215')] -preconfigopts = "libtoolize && aclocal && automake --add-missing && autoconf && " +preconfigopts = "aclocal && libtoolize && autoconf && automake --add-missing && " sanity_check_paths = { 'files': ['include/bitmask.h', 'lib/libbitmask.a', 'lib/libbitmask.so'], diff --git a/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb b/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb index 7f3929821a..51fb71266e 100644 --- a/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb +++ b/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_BZ2] builddependencies = [('Autotools', '20150215')] dependencies = [('libbitmask', '2.0')] -preconfigopts = "libtoolize && aclocal && mv configure.in configure.ac && automake --add-missing && autoconf && " +preconfigopts = "mv configure.in configure.ac && aclocal && libtoolize && autoconf && automake --add-missing && " sanity_check_paths = { 'files': ['include/cpuset.h', 'lib/libcpuset.a', 'lib/libcpuset.so'], -- GitLab From b61d10c1cdefa3fd25311e14331a3780d97ebeb3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 26 Aug 2016 14:59:25 +0200 Subject: [PATCH 242/701] use stable version 1.8.3 instead of unstable 1.9.1, remove automake autoconf libtool xz and add autotools --- ...6a.eb => GST-plugins-base-1.8.3-foss-2016a.eb} | 15 ++++++--------- ...oss-2016a.eb => GStreamer-1.8.3-foss-2016a.eb} | 3 +-- 2 files changed, 7 insertions(+), 11 deletions(-) rename easybuild/easyconfigs/g/GST-plugins-base/{GST-plugins-base-1.9.1-foss-2016a.eb => GST-plugins-base-1.8.3-foss-2016a.eb} (77%) rename easybuild/easyconfigs/g/GStreamer/{GStreamer-1.9.1-foss-2016a.eb => GStreamer-1.8.3-foss-2016a.eb} (94%) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb similarity index 77% rename from easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb rename to easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb index 16d3c00dec..7583a907a1 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.9.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GST-plugins-base' -version = '1.9.1' +version = '1.8.3' homepage = 'http://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling @@ -15,16 +15,13 @@ source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] dependencies = [ - ('GStreamer', '1.9.1'), - ('Automake', '1.15'), - ('Autoconf', '2.69'), - ('gettext', '0.19.7'), + ('GStreamer', '1.8.3'), + ('gettext', '0.19.7'), ] builddependencies = [ - ('XZ', '5.2.2', '-gettext-0.19.7'), - ('libtool', '2.4.6'), - ('pkgconfig', '1.1.0', '-Python-2.7.11'), + ('Autotools', '20150215'), + ('pkg-config', '1.1.0', '-Python-2.7.11'), ] sanity_check_paths = { @@ -38,4 +35,4 @@ modextrapaths = { 'XDG_DATA_DIRS': 'share', } -moduleclass = 'vis' +moduleclass = 'vis' \ No newline at end of file diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.9.1-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb similarity index 94% rename from easybuild/easyconfigs/g/GStreamer/GStreamer-1.9.1-foss-2016a.eb rename to easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb index 6fb42440e5..191ac52216 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.9.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.8.3-foss-2016a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GStreamer' -version = '1.9.1' +version = '1.8.3' homepage = 'http://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling @@ -20,7 +20,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -# does not work with Bison 3.x builddependencies = [ ('Bison', '3.0.4'), ] -- GitLab From 27fea3fcf0d7cd115c05c46ee2edac94b9a244c1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 26 Aug 2016 15:35:00 +0200 Subject: [PATCH 243/701] Added FFmpeg/3.1.3 --- .../f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb | 30 ++++++++++++++++++ .../x/x264/x264-20160614-intel-2016b.eb | 27 ++++++++++++++++ .../y/Yasm/Yasm-1.3.0-intel-2016b.eb | 31 +++++++++++++++++++ 3 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20160614-intel-2016b.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb new file mode 100644 index 0000000000..4dee167c84 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.1.3' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.02'), + ('zlib', '1.2.8'), + ('x264', '20160614'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +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/x/x264/x264-20160614-intel-2016b.eb b/easybuild/easyconfigs/x/x264/x264-20160614-intel-2016b.eb new file mode 100644 index 0000000000..d348640a5d --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160614-intel-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160614' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb new file mode 100644 index 0000000000..bd4bc5d66f --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.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 = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 05f59d21243238f0051c88719158ebe837dbaf45 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 26 Aug 2016 15:42:23 +0200 Subject: [PATCH 244/701] add easyconfig LLVM-3.8.1-GCCcore-4.9.3.eb --- .../easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index c964fa0788..be62c66c15 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -23,7 +23,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev')] # We hide this by default since users should not use it in production -hidden = True +#hidden = True # bare installation: only known module deps for GCCcore tools included exts_list =[] -- GitLab From fa42410fa567214974bc49f203f3c93fd835ea6e Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 26 Aug 2016 15:48:04 +0200 Subject: [PATCH 245/701] add easyconfig jhbuild-3.15.92-GCCcore-4.9.3.eb --- .../g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb | 9 ++++----- .../p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb index 8e1b03ad2a..cd97e3e99f 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb @@ -13,15 +13,14 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [ - ('binutils', '2.25'), -] +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' dependencies = [ ('libxml2', '2.9.4'), - ('ncurses', '6.0'), ] -configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' +builddependencies = [ + ('binutils', '2.25'), +] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index c964fa0788..be62c66c15 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -23,7 +23,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev')] # We hide this by default since users should not use it in production -hidden = True +#hidden = True # bare installation: only known module deps for GCCcore tools included exts_list =[] -- GitLab From f1f515f0a0d15546d2116aabc3827a350bf349b1 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 26 Aug 2016 15:51:31 +0200 Subject: [PATCH 246/701] add easyconfig jhbuild-3.15.92-GCCcore-4.9.3.eb --- .../g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb | 9 +++++---- .../j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb index cd97e3e99f..8e1b03ad2a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb @@ -13,14 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' +builddependencies = [ + ('binutils', '2.25'), +] dependencies = [ ('libxml2', '2.9.4'), + ('ncurses', '6.0'), ] -builddependencies = [ - ('binutils', '2.25'), -] +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb index 6cafa8acd8..9186755910 100644 --- a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -44,4 +44,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'lib' +moduleclass = 'tools' -- GitLab From 799511370e617339233dc9998632801b52685636 Mon Sep 17 00:00:00 2001 From: Alan Date: Fri, 26 Aug 2016 16:09:59 +0200 Subject: [PATCH 247/701] Update the comment for why it might be a good idea to hide the bare Python module --- .../easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index be62c66c15..ffcdc89a3a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -22,7 +22,8 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev')] -# We hide this by default since users should not use it in production +# We hide this by default since users should not use it in production, high-performance Python should be delivered at +# compiler level with a default extension set #hidden = True # bare installation: only known module deps for GCCcore tools included -- GitLab From 22346e9e0806b51649e4d0f8b37860a60471d359 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Aug 2016 16:51:29 +0200 Subject: [PATCH 248/701] Add custom sanity check path --- easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb index ab5263c53f..a702a8acce 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb @@ -34,4 +34,9 @@ configopts += "-DLLVM_INSTALL_UTILS=ON" separate_build_dir = True +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + moduleclass = 'compiler' -- GitLab From 661bca46603ec68ee41eb8a077e8aaa471b2e13c Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Aug 2016 16:54:54 +0200 Subject: [PATCH 249/701] Various minor tweaks --- .../easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index ffcdc89a3a..d460591e20 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -6,13 +6,14 @@ homepage = 'http://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." toolchain = {'name': 'GCCcore', 'version': '4.9.3'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} +toolchainopts = {'pic': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] dependencies = [ ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.14.1'), @@ -20,7 +21,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # We hide this by default since users should not use it in production, high-performance Python should be delivered at # compiler level with a default extension set -- GitLab From 4e6f940d30880beb6ec841e51b54d220b8387816 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2016 17:16:17 +0200 Subject: [PATCH 250/701] add easyconfig CheMPS2-1.8-intel-2016b.eb --- .../c/CheMPS2/CheMPS2-1.8-intel-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8-intel-2016b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8-intel-2016b.eb new file mode 100644 index 0000000000..f566c1ab13 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('HDF5', '1.8.17') +] + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' -- GitLab From 508c2ef263029a138cb5ea86228c863c239ee117 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Fri, 26 Aug 2016 16:39:23 +0100 Subject: [PATCH 251/701] CDO 1.7.1 and YAXT 0.4.4 built with foss 2015a --- .../easyconfigs/c/CDO/CDO-1.7.1-foss-2015a.eb | 28 +++++++++++++++++++ .../y/YAXT/YAXT-0.4.4-foss-2015a.eb | 22 +++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.7.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.4.4-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.7.1-foss-2015a.eb b/easybuild/easyconfigs/c/CDO/CDO-1.7.1-foss-2015a.eb new file mode 100644 index 0000000000..0f0ccdc373 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.7.1-foss-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.7.1' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://code.zmaw.de/attachments/download/12070/'] + +dependencies = [ + ('HDF5', '1.8.13'), + ('netCDF', '4.3.2'), + ('YAXT', '0.4.4'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF" + +sanity_check_paths = { + 'files': ["bin/cdo"], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.4.4-foss-2015a.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.4.4-foss-2015a.eb new file mode 100644 index 0000000000..c754d53b27 --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.4.4-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.4.4' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/464/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["include/yaxt.h", "include/yaxt.mod", "lib/libyaxt.a", "lib/libyaxt.%s" % SHLIB_EXT], + 'dirs': ["include/xt"], +} + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +moduleclass = 'tools' -- GitLab From 86d0c52feede1205a75e5712a10e3083e37f28ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2016 17:45:26 +0200 Subject: [PATCH 252/701] fix version in PETSc 3.7.3 easyconfigs + add --LIBS configure option --- .../p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb index a5fcbdc035..f3270387e0 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb @@ -1,5 +1,5 @@ name = 'PETSc' -version = '3.7.2' +version = '3.7.3' versionsuffix = '-Python-2.7.11' homepage = 'http://www.mcs.anl.gov/petsc' @@ -29,4 +29,6 @@ dependencies = [ builddependencies = [('CMake', '3.5.2')] +configopts = '--LIBS="$LIBS"' + moduleclass = 'numlib' -- GitLab From 955aef7fcca37e1ea5c5d78a8aae25752d75f470 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2016 19:37:07 +0200 Subject: [PATCH 253/701] specify correct MPI target in FDS easyconfigs --- easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb | 5 ++++- easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb | 5 +++++ easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 5 +++++ easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb | 5 +++++ easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb | 5 +++++ easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb | 5 +++++ 6 files changed, 29 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb index 7278d23d80..cda8fd4795 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb @@ -23,7 +23,10 @@ start_dir = 'FDS_Compilation' skipsteps = ['configure', 'install'] buildininstalldir = True -prebuildopts = 'env FFLAGS="$FFLAGS -fpp"' +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] modextrapaths = {'PATH': 'FDS_Compilation'} diff --git a/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb index 2779e0ddd8..8092c9cddd 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb @@ -23,6 +23,11 @@ parallel = 1 skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] + modextrapaths = {'PATH': 'FDS_Compilation'} sanity_check_paths = { 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 cefbd7a7f6..807c4c493a 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 @@ -17,6 +17,11 @@ patches = ['FDS-%(version)s_makefile.patch'] skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] + 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 bbf4065638..8cc7b51a0a 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 @@ -17,6 +17,11 @@ patches = ['FDS-%(version)s_makefile.patch'] skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] + modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb index e4ac832f81..9aee2bd190 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb @@ -17,6 +17,11 @@ patches = ['FDS-%(version)s_makefile.patch'] skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] + modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb index 75d4dcf42f..296e2d6beb 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb @@ -21,6 +21,11 @@ start_dir = 'FDS_Compilation' skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] + modextrapaths = {'PATH': 'FDS_Compilation'} sanity_check_paths = { -- GitLab From ff01f5cb0a9c8637d01d2aa96e6fbf250b87505c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2016 19:40:52 +0200 Subject: [PATCH 254/701] correct postinstallcmds for older FDS versions --- easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 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 807c4c493a..ffcd0bf206 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 @@ -20,7 +20,7 @@ buildininstalldir = True target = 'mpi_intel_linux_64' buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target -postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] +postinstallcmds = ["ln -s %%(installdir)s/FDS_Source/fds_%s %%(installdir)s/FDS_Source/fds" % target] modextrapaths = {'PATH': 'FDS_Source'} 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 8cc7b51a0a..4ebe2f2b99 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 @@ -20,7 +20,7 @@ buildininstalldir = True target = 'mpi_intel_linux_64' buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target -postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] +postinstallcmds = ["ln -s %%(installdir)s/FDS_Source/fds_%s %%(installdir)s/FDS_Source/fds" % target] modextrapaths = {'PATH': 'FDS_Source'} diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb index 9aee2bd190..ea711d7ff3 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb @@ -20,7 +20,7 @@ buildininstalldir = True target = 'mpi_intel_linux_64' buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target -postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] +postinstallcmds = ["ln -s %%(installdir)s/FDS_Source/fds_%s %%(installdir)s/FDS_Source/fds" % target] modextrapaths = {'PATH': 'FDS_Source'} -- GitLab From 3cb609f2d4f7ef66903346d826bd79f305e1ecd7 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 26 Aug 2016 20:16:06 +0200 Subject: [PATCH 255/701] Add binutils as dep ...since python may be called on its own --- .../easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index d460591e20..c12401c785 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -12,6 +12,7 @@ source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] dependencies = [ + ('binutils', '2.25'), ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('libreadline', '6.3'), -- GitLab From 5d3104c7e3f63a5cd357a639d3b31e97a9a67b6e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 26 Aug 2016 21:00:56 +0200 Subject: [PATCH 256/701] Fix to let GCC build with ISL Don't link with -lmpc and -lmpfr to find libisl --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index 83a80912f2..5460677b1f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -33,7 +33,10 @@ builddependencies = [ ('binutils', '2.27'), ] -patches = [('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +patches = [ + ('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), + '%(name)s-%(version)s-fix-find-isl.patch', +] checksums = [ '8fb6cb98b8459f5863328380fbf06bd1', # gcc-6.1.0.tar.bz2 @@ -42,11 +45,12 @@ checksums = [ 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 '13a670dca515e905856f95d13697fcdd', # mpfr-3.1.2-allpatches-20160522.patch + 'ec9dec1104d76bf0c60bf38ec14ac4a8', # GCCcore-6.1.0-fix-find-isl.patch ] languages = ['c', 'c++', 'fortran'] -withisl = False +withisl = True # building GCC sometimes fails if make parallelism is too high, so let's limit it maxparallel = 4 -- GitLab From a8f3055658aac02d675254710ed6d7ad67fa8226 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 26 Aug 2016 21:21:39 +0200 Subject: [PATCH 257/701] Now actually add patch --- .../g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch new file mode 100644 index 0000000000..2af885f998 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch @@ -0,0 +1,13 @@ +# Don't use libmpc and libmpfr to find libisl +diff -ur gcc-6.1.0/configure gcc-6.1.0.orig/configure +--- gcc-6.1.0/configure 2016-08-26 17:51:48.470524515 +0200 ++++ gcc-6.1.0.orig/configure 2016-03-17 23:54:19.000000000 +0100 +@@ -6018,7 +6018,7 @@ + _isl_saved_LIBS=$LIBS + + CFLAGS="${_isl_saved_CFLAGS} ${islinc} ${gmpinc}" +- LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs}" ++ LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs} ${gmplibs}" + LIBS="${_isl_saved_LIBS} -lisl -lgmp" + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for isl 0.16, 0.15, or deprecated 0.14" >&5 -- GitLab From d4d5b5026162c140a5b37e5fa41e03ea25c37370 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Aug 2016 11:13:52 +0200 Subject: [PATCH 258/701] Use correct patch for GCCcore/6.1.0 --- .../g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch index 2af885f998..60c1335534 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch @@ -1,13 +1,13 @@ # Don't use libmpc and libmpfr to find libisl -diff -ur gcc-6.1.0/configure gcc-6.1.0.orig/configure ---- gcc-6.1.0/configure 2016-08-26 17:51:48.470524515 +0200 -+++ gcc-6.1.0.orig/configure 2016-03-17 23:54:19.000000000 +0100 +diff -ur gcc-6.1.0.orig/configure gcc-6.1.0/configure +--- gcc-6.1.0.orig/configure 2016-08-26 17:51:48.470524515 +0200 ++++ gcc-6.1.0/configure 2016-03-17 23:54:19.000000000 +0100 @@ -6018,7 +6018,7 @@ _isl_saved_LIBS=$LIBS CFLAGS="${_isl_saved_CFLAGS} ${islinc} ${gmpinc}" -- LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs}" -+ LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs} ${gmplibs}" +- LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs} ${gmplibs}" ++ LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs}" LIBS="${_isl_saved_LIBS} -lisl -lgmp" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for isl 0.16, 0.15, or deprecated 0.14" >&5 -- GitLab From cebcd6b85dc662750c32c32284abfde950b025fe Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 27 Aug 2016 11:23:10 +0200 Subject: [PATCH 259/701] Fix checksum of patch --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index 5460677b1f..3d848e83be 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -45,7 +45,7 @@ checksums = [ 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 '13a670dca515e905856f95d13697fcdd', # mpfr-3.1.2-allpatches-20160522.patch - 'ec9dec1104d76bf0c60bf38ec14ac4a8', # GCCcore-6.1.0-fix-find-isl.patch + '8551e7d4b099751e4bc34fca5cd400f4', # GCCcore-6.1.0-fix-find-isl.patch ] languages = ['c', 'c++', 'fortran'] -- GitLab From dc39cdfdb641005d18c89f1fc148cabacc15bec0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sat, 27 Aug 2016 22:33:15 +0200 Subject: [PATCH 260/701] provide patch for hardcoded CC --- .../easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch new file mode 100644 index 0000000000..51b4ca18e5 --- /dev/null +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch @@ -0,0 +1,13 @@ +subtitue hardcoded cc for gcc to prevent 'cc1: error: unrecognized command line option "-fstack-protector-strong"' +author: Ruben van Dijk (University of Groningen) +--- Makefile.orig 2016-08-27 11:42:01.000000000 +0200 ++++ Makefile 2016-08-27 11:36:53.000000000 +0200 +@@ -34,7 +34,7 @@ + # These definitions are from config.sh (via /software/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/Config.pm). + # They may have been overridden via Makefile.PL or on the command line. + AR = ar +-CC = gcc ++CC = cc + CCCDLFLAGS = -fPIC + CCDLFLAGS = -Wl,-E + DLEXT = so -- GitLab From acb8685ebec479541fe3e5b1b42720122c23d2bd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 09:25:36 +0200 Subject: [PATCH 261/701] Boost without Python --- easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb index 370bb22280..67f6199614 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb @@ -15,6 +15,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--without-libraries=python' + # also build boost_mpi boost_mpi = True -- GitLab From d58c78075f93ba3cc9aa18c92933e9ebee5d4dba Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 09:26:20 +0200 Subject: [PATCH 262/701] Use ParaView/5.1.2 in OpenFOAM/4.0 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb index 811d45648a..0caa9fc8da 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb @@ -16,7 +16,7 @@ sources = [ 'ThirdParty-%(version)s.tgz', ] -paraversion = '5.1.0' +paraversion = '5.1.2' patches = [ 'OpenFOAM-%(version)s_cleanup.patch', 'OpenFOAM-%(version)s_libreadline.patch', -- GitLab From 3ce90814d8f05b8c4be8a07c0a343fd49db87ed6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 09:27:15 +0200 Subject: [PATCH 263/701] Update ParaView to 5.1.2 --- ...1.0-intel-2016b-mpi.eb => ParaView-5.1.2-intel-2016b-mpi.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/ParaView/{ParaView-5.1.0-intel-2016b-mpi.eb => ParaView-5.1.2-intel-2016b-mpi.eb} (99%) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.0-intel-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb similarity index 99% rename from easybuild/easyconfigs/p/ParaView/ParaView-5.1.0-intel-2016b-mpi.eb rename to easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb index efcf03805f..bb0153d900 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.0-intel-2016b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'ParaView' -version = '5.1.0' +version = '5.1.2' versionsuffix = '-mpi' homepage = "http://www.paraview.org" -- GitLab From ff3acb44938dfb493e18eb15683b6da943b43249 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 09:29:34 +0200 Subject: [PATCH 264/701] Update to GCC/6.2 --- .../g/GCC/{GCC-6.1.0-2.27.eb => GCC-6.2.0-2.27.eb} | 2 +- ....0-fix-find-isl.patch => GCCcore-6.1.2-fix-find-isl.patch} | 0 .../g/GCCcore/{GCCcore-6.1.0.eb => GCCcore-6.2.0.eb} | 4 ++-- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/GCC/{GCC-6.1.0-2.27.eb => GCC-6.2.0-2.27.eb} (97%) rename easybuild/easyconfigs/g/GCCcore/{GCCcore-6.1.0-fix-find-isl.patch => GCCcore-6.1.2-fix-find-isl.patch} (100%) rename easybuild/easyconfigs/g/GCCcore/{GCCcore-6.1.0.eb => GCCcore-6.2.0.eb} (95%) diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.2.0-2.27.eb similarity index 97% rename from easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb rename to easybuild/easyconfigs/g/GCC/GCC-6.2.0-2.27.eb index 4faa0a48e8..645cbb0314 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-6.2.0-2.27.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'GCC' -version = '6.1.0' +version = '6.2.0' binutilsver = '2.27' versionsuffix = '-%s' % binutilsver diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.2-fix-find-isl.patch similarity index 100% rename from easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0-fix-find-isl.patch rename to easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.2-fix-find-isl.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb similarity index 95% rename from easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb rename to easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 3d848e83be..0671ba969c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'EB_GCC' name = 'GCCcore' -version = '6.1.0' +version = '6.2.0' homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, @@ -45,7 +45,7 @@ checksums = [ 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 '13a670dca515e905856f95d13697fcdd', # mpfr-3.1.2-allpatches-20160522.patch - '8551e7d4b099751e4bc34fca5cd400f4', # GCCcore-6.1.0-fix-find-isl.patch + '8551e7d4b099751e4bc34fca5cd400f4', # GCCcore-6.2.0-fix-find-isl.patch ] languages = ['c', 'c++', 'fortran'] -- GitLab From 7f91057e8b00d5dc07bc421bcd0ae9a2e1d5b112 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 09:35:03 +0200 Subject: [PATCH 265/701] Sync all deps to GCCcore/6.2 --- ...ison-3.0.4-GCCcore-6.1.0.eb => Bison-3.0.4-GCCcore-6.2.0.eb} | 2 +- ...ils-2.27-GCCcore-6.1.0.eb => binutils-2.27-GCCcore-6.2.0.eb} | 2 +- ...{flex-2.6.0-GCCcore-6.1.0.eb => flex-2.6.0-GCCcore-6.2.0.eb} | 2 +- .../{M4-1.4.17-GCCcore-6.1.0.eb => M4-1.4.17-GCCcore-6.2.0.eb} | 2 +- ...{zlib-1.2.8-GCCcore-6.1.0.eb => zlib-1.2.8-GCCcore-6.2.0.eb} | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/b/Bison/{Bison-3.0.4-GCCcore-6.1.0.eb => Bison-3.0.4-GCCcore-6.2.0.eb} (92%) rename easybuild/easyconfigs/b/binutils/{binutils-2.27-GCCcore-6.1.0.eb => binutils-2.27-GCCcore-6.2.0.eb} (90%) rename easybuild/easyconfigs/f/flex/{flex-2.6.0-GCCcore-6.1.0.eb => flex-2.6.0-GCCcore-6.2.0.eb} (91%) rename easybuild/easyconfigs/m/M4/{M4-1.4.17-GCCcore-6.1.0.eb => M4-1.4.17-GCCcore-6.2.0.eb} (93%) rename easybuild/easyconfigs/z/zlib/{zlib-1.2.8-GCCcore-6.1.0.eb => zlib-1.2.8-GCCcore-6.2.0.eb} (93%) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb similarity index 92% rename from easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb rename to easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb index 85a3abd7ad..e30337e6ba 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb @@ -7,7 +7,7 @@ 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': 'GCCcore', 'version': '6.1.0'} +toolchain = {'name': 'GCCcore', 'version': '6.2.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb similarity index 90% rename from easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb rename to easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb index 4c7f93641a..354c4bdea8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb @@ -4,7 +4,7 @@ version = '2.27' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'GCCcore', 'version': '6.1.0'} +toolchain = {'name': 'GCCcore', 'version': '6.2.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb similarity index 91% rename from easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb rename to easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb index 687cf19d5f..76aba74a8b 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb @@ -5,7 +5,7 @@ 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': 'GCCcore', 'version': '6.1.0'} +toolchain = {'name': 'GCCcore', 'version': '6.2.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb similarity index 93% rename from easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb rename to easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb index 2bc1e5e46b..6f774b05e4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb @@ -8,7 +8,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce 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': 'GCCcore', 'version': '6.1.0'} +toolchain = {'name': 'GCCcore', 'version': '6.2.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb similarity index 93% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb rename to easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb index 47a40a4035..ecd6eff1be 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb @@ -8,7 +8,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.""" -toolchain = {'name': 'GCCcore', 'version': '6.1.0'} +toolchain = {'name': 'GCCcore', 'version': '6.2.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -- GitLab From 5875302710e72ea6a236069397fd5dd20d7c0ae2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 09:45:53 +0200 Subject: [PATCH 266/701] Fix checksum for GCC/6.2 --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 0671ba969c..eb4cda715a 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -39,7 +39,7 @@ patches = [ ] checksums = [ - '8fb6cb98b8459f5863328380fbf06bd1', # gcc-6.1.0.tar.bz2 + '9768625159663b300ae4de2f4745fcc4', # gcc-6.2.0.tar.bz2 '4c175f86e11eb32d8bf9872ca3a8e11d', # gmp-6.1.1.tar.bz2 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.tar.gz 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz -- GitLab From 02c3a88862dcbbfaad1d6d5ec270ab8498056d14 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 09:48:09 +0200 Subject: [PATCH 267/701] Drop checksum for local patch --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index eb4cda715a..293df06f75 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -45,7 +45,6 @@ checksums = [ 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 '13a670dca515e905856f95d13697fcdd', # mpfr-3.1.2-allpatches-20160522.patch - '8551e7d4b099751e4bc34fca5cd400f4', # GCCcore-6.2.0-fix-find-isl.patch ] languages = ['c', 'c++', 'fortran'] -- GitLab From e302fcb816a06ef2f1e1598c4afd7db10d5aebec Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 09:53:10 +0200 Subject: [PATCH 268/701] Rename patch correctly --- ...-6.1.2-fix-find-isl.patch => GCCcore-6.2.0-fix-find-isl.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/GCCcore/{GCCcore-6.1.2-fix-find-isl.patch => GCCcore-6.2.0-fix-find-isl.patch} (100%) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.2-fix-find-isl.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0-fix-find-isl.patch similarity index 100% rename from easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.2-fix-find-isl.patch rename to easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0-fix-find-isl.patch -- GitLab From 166381254983778e5360657b1051731f03e89437 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 10:10:34 +0200 Subject: [PATCH 269/701] Fix Mesa version --- .../easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb index bb0153d900..3fba0f0166 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb @@ -18,7 +18,7 @@ sources = ["ParaView-v%(version)s-source.tar.gz"] dependencies = [ ('X11', '20160819'), - ('Mesa', '12.0.0'), + ('Mesa', '12.0.1'), ('libGLU', '9.0.0'), ('Qt', '4.8.7'), ('zlib', '1.2.8'), -- GitLab From 113096cd051abf210a6b4c3d9de039319552a6c3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 29 Aug 2016 10:26:19 +0200 Subject: [PATCH 270/701] update patch file --- .../PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 5 ++++- .../p/PSORTb/PSORTb-3.0.4-libpsortb.patch | 4 ++-- .../easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch | 14 +++++++------- 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index 9a447b3dd9..6da5f456df 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.psort.org/download/'] sources = ['bio-tools-psort-all.%(version)s.tar.gz'] -patches = ['PSORTb-%(version)s-libpsortb.patch'] +patches = [ + 'PSORTb-%(version)s-libpsortb.patch', + 'PSORTb-%(version)s_CC.patch', +] dependencies = [ ('Perl', '5.22.1'), diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch index 4272ae4de8..bbc5e91be1 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch @@ -1,5 +1,5 @@ -# Removed q and a and perl scripting environment set accordingly. -# Author: Fokke Dijkstra - Rijksuniversiteit Groningen (RUG) +Removed q and a and perl scripting environment set accordingly. +Author: Fokke Dijkstra (University of Groningen) diff -ru bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm --- bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm 2010-07-29 00:12:43.000000000 +0200 +++ bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm 2015-11-26 13:50:18.000000000 +0100 diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch index 51b4ca18e5..54f95f9b0d 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch @@ -1,13 +1,13 @@ -subtitue hardcoded cc for gcc to prevent 'cc1: error: unrecognized command line option "-fstack-protector-strong"' -author: Ruben van Dijk (University of Groningen) ---- Makefile.orig 2016-08-27 11:42:01.000000000 +0200 -+++ Makefile 2016-08-27 11:36:53.000000000 +0200 +#Subtitue hardcoded cc for gcc to prevent 'cc1: error: unrecognized command line option "-fstack-protector-strong"' +#Author: Ruben van Dijk (University of Groningen) +--- bio-tools-psort-all/bio-tools-psort-modhmm/Makefile 2016-08-29 09:40:30.000000000 +0200 ++++ bio-tools-psort-all/bio-tools-psort-modhmm/Makefile 2016-08-29 09:40:14.000000000 +0200 @@ -34,7 +34,7 @@ # These definitions are from config.sh (via /software/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/Config.pm). # They may have been overridden via Makefile.PL or on the command line. AR = ar --CC = gcc -+CC = cc +-CC = cc ++CC = gcc CCCDLFLAGS = -fPIC CCDLFLAGS = -Wl,-E - DLEXT = so + DLEXT = so \ No newline at end of file -- GitLab From 435287aa309e0e88d0dcc159366b50136031157c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 10:39:32 +0200 Subject: [PATCH 271/701] Fix remarks --- easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.27.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb index 354c4bdea8..88e16771df 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb @@ -12,7 +12,7 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, 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-2.27.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb index 3309ac61a8..6011a78009 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb @@ -12,7 +12,7 @@ source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] -- GitLab From f1fce403abf9e383dc2697e7fb5cdea54cf4383a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 10:53:02 +0200 Subject: [PATCH 272/701] Fix more remarks --- .../GCCcore/GCCcore-6.2.0-fix-find-isl.patch | 1 + .../mpfr-3.1.4-allpatches-20160804.patch | 46 ++++++++++--------- 2 files changed, 25 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0-fix-find-isl.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0-fix-find-isl.patch index 60c1335534..6334b6be35 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0-fix-find-isl.patch +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0-fix-find-isl.patch @@ -1,4 +1,5 @@ # Don't use libmpc and libmpfr to find libisl +# by wpoely86@gmail.com diff -ur gcc-6.1.0.orig/configure gcc-6.1.0/configure --- gcc-6.1.0.orig/configure 2016-08-26 17:51:48.470524515 +0200 +++ gcc-6.1.0/configure 2016-03-17 23:54:19.000000000 +0100 diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160804.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160804.patch index bcb2138fdf..5823cecfe6 100644 --- a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160804.patch +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160804.patch @@ -1,3 +1,5 @@ +# All mpfr patches as of 2016-08-04 +# taken from their website: http://www.mpfr.org/mpfr-current/#download diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES --- mpfr-3.1.4-a/PATCHES 2016-04-13 21:22:23.720604013 +0000 +++ mpfr-3.1.4-b/PATCHES 2016-04-13 21:22:23.744603677 +0000 @@ -15,7 +17,7 @@ diff -Naurd mpfr-3.1.4-a/src/mpfr-impl.h mpfr-3.1.4-b/src/mpfr-impl.h @@ -252,19 +252,6 @@ # define MPFR_WIN_THREAD_SAFE_DLL 1 #endif - + -/* Detect some possible inconsistencies under Unix. */ -#if defined(__unix__) -# if defined(_WIN32) @@ -41,7 +43,7 @@ diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h #define MPFR_VERSION_PATCHLEVEL 4 -#define MPFR_VERSION_STRING "3.1.4" +#define MPFR_VERSION_STRING "3.1.4-p1" - + /* Macros dealing with MPFR VERSION */ #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c @@ -85,7 +87,7 @@ diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h #define MPFR_VERSION_PATCHLEVEL 4 -#define MPFR_VERSION_STRING "3.1.4-p1" +#define MPFR_VERSION_STRING "3.1.4-p2" - + /* Macros dealing with MPFR VERSION */ #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) diff -Naurd mpfr-3.1.4-a/src/sub_ui.c mpfr-3.1.4-b/src/sub_ui.c @@ -113,27 +115,27 @@ diff -Naurd mpfr-3.1.4-a/tests/tadd_ui.c mpfr-3.1.4-b/tests/tadd_ui.c --- mpfr-3.1.4-a/tests/tadd_ui.c 2016-03-06 11:33:03.000000000 +0000 +++ mpfr-3.1.4-b/tests/tadd_ui.c 2016-05-22 19:59:43.854399385 +0000 @@ -69,7 +69,9 @@ - + /* nan + 2394875 == nan */ mpfr_set_nan (x); + mpfr_clear_nanflag (); mpfr_add_ui (y, x, 2394875L, MPFR_RNDN); + MPFR_ASSERTN (mpfr_nanflag_p ()); MPFR_ASSERTN (mpfr_nan_p (y)); - + /* +inf + 2394875 == +inf */ diff -Naurd mpfr-3.1.4-a/tests/tsub_ui.c mpfr-3.1.4-b/tests/tsub_ui.c --- mpfr-3.1.4-a/tests/tsub_ui.c 2016-03-06 11:33:03.000000000 +0000 +++ mpfr-3.1.4-b/tests/tsub_ui.c 2016-05-22 19:59:43.854399385 +0000 @@ -96,7 +96,9 @@ - + /* nan - 1 == nan */ mpfr_set_nan (x); + mpfr_clear_nanflag (); mpfr_sub_ui (y, x, 1L, MPFR_RNDN); + MPFR_ASSERTN (mpfr_nanflag_p ()); MPFR_ASSERTN (mpfr_nan_p (y)); - + /* +inf - 1 == +inf */ diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES --- mpfr-3.1.4-a/PATCHES 2016-06-01 13:00:30.748711490 +0000 @@ -155,7 +157,7 @@ diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h #define MPFR_VERSION_PATCHLEVEL 4 -#define MPFR_VERSION_STRING "3.1.4-p2" +#define MPFR_VERSION_STRING "3.1.4-p3" - + /* Macros dealing with MPFR VERSION */ #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) diff -Naurd mpfr-3.1.4-a/src/sub1.c mpfr-3.1.4-b/src/sub1.c @@ -213,7 +215,7 @@ diff -Naurd mpfr-3.1.4-a/tests/tsub.c mpfr-3.1.4-b/tests/tsub.c @@ -630,6 +630,135 @@ } } - + +static void +check_max_almosteven (void) +{ @@ -374,7 +376,7 @@ diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h #define MPFR_VERSION_PATCHLEVEL 4 -#define MPFR_VERSION_STRING "3.1.4-p3" +#define MPFR_VERSION_STRING "3.1.4-p4" - + /* Macros dealing with MPFR VERSION */ #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c @@ -391,45 +393,45 @@ diff -Naurd mpfr-3.1.4-a/tests/tpow_z.c mpfr-3.1.4-b/tests/tpow_z.c --- mpfr-3.1.4-a/tests/tpow_z.c 2016-03-06 11:33:03.000000000 +0000 +++ mpfr-3.1.4-b/tests/tpow_z.c 2016-08-04 20:41:14.113592494 +0000 @@ -26,7 +26,7 @@ - + #include "mpfr-test.h" - + -#define ERROR(str) do { printf("Error for "str"\n"); exit (1); } while (0) +#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) - + static void check_special (void) diff -Naurd mpfr-3.1.4-a/tests/tset_si.c mpfr-3.1.4-b/tests/tset_si.c --- mpfr-3.1.4-a/tests/tset_si.c 2016-03-06 11:33:03.000000000 +0000 +++ mpfr-3.1.4-b/tests/tset_si.c 2016-08-04 20:41:14.113592494 +0000 @@ -26,7 +26,7 @@ - + #include "mpfr-test.h" - + -#define ERROR(str) {printf("Error for "str"\n"); exit(1);} +#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) - + static void test_2exp (void) diff -Naurd mpfr-3.1.4-a/tests/tset_sj.c mpfr-3.1.4-b/tests/tset_sj.c --- mpfr-3.1.4-a/tests/tset_sj.c 2016-03-06 11:33:03.000000000 +0000 +++ mpfr-3.1.4-b/tests/tset_sj.c 2016-08-04 20:41:14.113592494 +0000 @@ -42,7 +42,7 @@ - + #else - + -#define ERROR(str) {printf("Error for "str"\n"); exit(1);} +#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) - + static int inexact_sign (int x) diff -Naurd mpfr-3.1.4-a/tests/tsi_op.c mpfr-3.1.4-b/tests/tsi_op.c --- mpfr-3.1.4-a/tests/tsi_op.c 2016-03-06 11:33:03.000000000 +0000 +++ mpfr-3.1.4-b/tests/tsi_op.c 2016-08-04 20:41:14.113592494 +0000 @@ -26,14 +26,16 @@ - + #include "mpfr-test.h" - + -#define ERROR1(s, i, z, exp) \ -{\ - printf("Error for "s" and i=%d\n", i);\ @@ -448,6 +450,6 @@ diff -Naurd mpfr-3.1.4-a/tests/tsi_op.c mpfr-3.1.4-b/tests/tsi_op.c + exit(1); \ + } \ + while (0) - + const struct { const char * op1; -- GitLab From c59630b9d1d632553c4cc362d349720da0589152 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 29 Aug 2016 10:55:24 +0200 Subject: [PATCH 273/701] Patch for rotor tests --- .../openbabel-2.3.2-comparison.patch | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/openbabel-2.3.2-comparison.patch diff --git a/easybuild/easyconfigs/o/OpenBabel/openbabel-2.3.2-comparison.patch b/easybuild/easyconfigs/o/OpenBabel/openbabel-2.3.2-comparison.patch new file mode 100644 index 0000000000..07b07de115 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/openbabel-2.3.2-comparison.patch @@ -0,0 +1,58 @@ +# From: https://sourceforge.net/p/openbabel/bugs/945/ +# Rotor tests fail on ppc architecture, because the checks for the expected value don't take into account the modulus. This patch should fix the issue. +# Author: Susi Lehtola +diff -up openbabel-2.3.2/include/openbabel/obutil.h.orig openbabel-2.3.2/include/openbabel/obutil.h +--- openbabel-2.3.2/include/openbabel/obutil.h.orig 2010-10-09 19:05:12.000000000 -0700 ++++ openbabel-2.3.2/include/openbabel/obutil.h 2014-10-16 16:35:49.050074389 -0700 +@@ -190,6 +190,8 @@ namespace OpenBabel + * \deprecated Use IsApprox() instead + */ + OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ++ //! Same but with comparison with a modulus ++ OBAPI bool IsNear_mod(const double &, const double &, const double & mod, const double epsilon=2e-6); + /*! "Safe" comparison for floats/doubles: true if a is less than epsilon + * This function really doesn't make any sense w.r.t. floating-point + * representation, so you should never use it. It is provided only for +diff -up openbabel-2.3.2/src/obutil.cpp.orig openbabel-2.3.2/src/obutil.cpp +--- openbabel-2.3.2/src/obutil.cpp.orig 2012-10-03 12:08:15.000000000 -0700 ++++ openbabel-2.3.2/src/obutil.cpp 2014-10-16 16:54:18.309740019 -0700 +@@ -77,6 +77,18 @@ namespace OpenBabel + return (fabs(a - b) < epsilon); + } + ++ //! Comparison for doubles with a modulus: returns mod(a - b,m) < epsilon ++ bool IsNear_mod(const double &a, const double &b, const double &m, const double epsilon) ++ { ++ double arg=a-b; ++ while(arg<-m/2) ++ arg+=m; ++ while(arg>=m/2) ++ arg-=m; ++ ++ return (fabs(arg) < epsilon); ++ } ++ + //! Comparison for doubles: returns fabs(a) < epsilon + bool IsNearZero(const double &a, const double epsilon) + { +diff -up openbabel-2.3.2/test/rotortest.cpp.orig openbabel-2.3.2/test/rotortest.cpp +--- openbabel-2.3.2/test/rotortest.cpp.orig 2011-10-12 13:24:02.000000000 -0700 ++++ openbabel-2.3.2/test/rotortest.cpp 2014-10-16 16:54:32.869985348 -0700 +@@ -74,7 +74,7 @@ void testOBRotorSetToAngle() + atoms[i] = (atoms[i] - 1) * 3; + rotor.SetRotAtoms(atoms); + +- OB_ASSERT(IsNear(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 1.0)); ++ OB_ASSERT(IsNear_mod(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 360.0, 1.0)); + + // rotate + rotor.SetToAngle(mol->GetCoordinates(), 60.0 * DEG_TO_RAD); +@@ -106,7 +106,7 @@ void testOBRotorSetRotor() + atoms[i] = (atoms[i] - 1) * 3; + rotor.SetRotAtoms(atoms); + +- OB_ASSERT(IsNear(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 1.0)); ++ OB_ASSERT(IsNear_mod(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 360.0, 1.0)); + rotor.SetToAngle(mol->GetCoordinates(), 60.0 * DEG_TO_RAD); + + // set torsion values -- GitLab From 75b81bb972304e081680b9c2d4c87f04a41ba8ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Aug 2016 11:13:50 +0200 Subject: [PATCH 274/701] fix taget for FDS with goolf, don't use -fpp for FDS r18915 --- easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb | 2 +- 3 files changed, 4 insertions(+), 4 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 ffcd0bf206..0c347df7a3 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 @@ -17,8 +17,8 @@ patches = ['FDS-%(version)s_makefile.patch'] skipsteps = ['configure', 'install'] buildininstalldir = True -target = 'mpi_intel_linux_64' -buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target +target = 'mpi_gnu_linux' +buildopts = '%s FFLAGS="$FFLAGS" FCOMPL="$FC"' % target postinstallcmds = ["ln -s %%(installdir)s/FDS_Source/fds_%s %%(installdir)s/FDS_Source/fds" % target] 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 4ebe2f2b99..13b8f521af 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 @@ -18,7 +18,7 @@ skipsteps = ['configure', 'install'] buildininstalldir = True target = 'mpi_intel_linux_64' -buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target +buildopts = '%s FFLAGS="$FFLAGS" FCOMPL="$FC"' % target postinstallcmds = ["ln -s %%(installdir)s/FDS_Source/fds_%s %%(installdir)s/FDS_Source/fds" % target] diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb index ea711d7ff3..26071db4b5 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb @@ -18,7 +18,7 @@ skipsteps = ['configure', 'install'] buildininstalldir = True target = 'mpi_intel_linux_64' -buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target +buildopts = '%s FFLAGS="$FFLAGS" FCOMPL="$FC"' % target postinstallcmds = ["ln -s %%(installdir)s/FDS_Source/fds_%s %%(installdir)s/FDS_Source/fds" % target] -- GitLab From 48ab0a0d3b81af0900d800c004bbfae5f73459a1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 11:51:27 +0200 Subject: [PATCH 275/701] Don't use checksums for local patches --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 293df06f75..011920e0f4 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -44,7 +44,6 @@ checksums = [ 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.tar.gz 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 - '13a670dca515e905856f95d13697fcdd', # mpfr-3.1.2-allpatches-20160522.patch ] languages = ['c', 'c++', 'fortran'] -- GitLab From b014ddf24e16ff69e2c92e847b56a16c64280b9c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 29 Aug 2016 11:57:19 +0200 Subject: [PATCH 276/701] rename patch --- ...el-2.3.2-comparison.patch => OpenBabel-2.3.2-comparison.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/o/OpenBabel/{openbabel-2.3.2-comparison.patch => OpenBabel-2.3.2-comparison.patch} (100%) diff --git a/easybuild/easyconfigs/o/OpenBabel/openbabel-2.3.2-comparison.patch b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-comparison.patch similarity index 100% rename from easybuild/easyconfigs/o/OpenBabel/openbabel-2.3.2-comparison.patch rename to easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-comparison.patch -- GitLab From 8ecf63fcaa31f4b5c755a31df54839aa5fc2e6c8 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 29 Aug 2016 11:57:44 +0200 Subject: [PATCH 277/701] rename patch --- .../o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb index 5289372a0b..1aafb42367 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb @@ -17,6 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenBabel-%(version)s-fix-link-path-tests.patch', 'OpenBabel-%(version)s-ignore-failed-test.patch', + 'OpenBabel-%(version)s-comparison.patch', ] builddependencies = [ -- GitLab From 26042f44687748880ba59fb8e49048a7c02c5093 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 29 Aug 2016 12:00:18 +0200 Subject: [PATCH 278/701] Update patch to inherit value from env --- easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch index 54f95f9b0d..7bd94606e9 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch @@ -7,7 +7,7 @@ # They may have been overridden via Makefile.PL or on the command line. AR = ar -CC = cc -+CC = gcc ++CC ?= gcc CCCDLFLAGS = -fPIC CCDLFLAGS = -Wl,-E - DLEXT = so \ No newline at end of file + DLEXT = so -- GitLab From 0e0d8ef4f51d797ad4e6e1f306f3165aed7b6e8c Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 29 Aug 2016 12:33:01 +0200 Subject: [PATCH 279/701] lrt flag --- .../easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb index f3270387e0..140e2b5ff8 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb @@ -29,6 +29,6 @@ dependencies = [ builddependencies = [('CMake', '3.5.2')] -configopts = '--LIBS="$LIBS"' +configopts = '--LIBS="$LIBS" -lrt' moduleclass = 'numlib' -- GitLab From 4f601d46f8f3283914e00d5e3bbba07610ca423d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 12:53:14 +0200 Subject: [PATCH 280/701] Workaround icpc bug for Qt5/5.7.0 and intel/2016b --- .../q/Qt5/Qt5-5.7.0-intel-2016b.eb | 2 + .../q/Qt5/Qt5-5.7.0-workaround-icpc-bug.patch | 62 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-workaround-icpc-bug.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb index 139d66073b..0710553732 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb @@ -14,6 +14,8 @@ source_urls = [ ] sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] +patches = ['%(name)s-%(version)s-workaround-icpc-bug.patch'] + builddependencies = [ ('pkg-config', '0.29.1'), ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-workaround-icpc-bug.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-workaround-icpc-bug.patch new file mode 100644 index 0000000000..fd58176f43 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-workaround-icpc-bug.patch @@ -0,0 +1,62 @@ +# This is an ugly workaround for a icpc bug: https://software.intel.com/en-us/comment/1882560 +# If the struct/class is local, icpc gives a faulty error. We move the class to be non-local. +# Remove this patch as soon as icpc is fixed. +# Ward Poelmans +diff -ur qt-everywhere-opensource-src-5.7.0.orig/qtdeclarative/src/quick/items/qquickitemanimation.cpp qt-everywhere-opensource-src-5.7.0/qtdeclarative/src/quick/items/qquickitemanimation.cpp +--- qt-everywhere-opensource-src-5.7.0.orig/qtdeclarative/src/quick/items/qquickitemanimation.cpp 2016-06-11 14:05:08.000000000 +0200 ++++ qt-everywhere-opensource-src-5.7.0/qtdeclarative/src/quick/items/qquickitemanimation.cpp 2016-08-29 12:42:35.880738297 +0200 +@@ -200,6 +200,27 @@ + } + } + ++struct QQuickParentAnimationData : public QAbstractAnimationAction ++{ ++ QQuickParentAnimationData() : reverse(false) {} ++ ~QQuickParentAnimationData() { qDeleteAll(pc); } ++ ++ QQuickStateActions actions; ++ //### reverse should probably apply on a per-action basis ++ bool reverse; ++ QList pc; ++ void doAction() Q_DECL_OVERRIDE ++ { ++ for (int ii = 0; ii < actions.count(); ++ii) { ++ const QQuickStateAction &action = actions.at(ii); ++ if (reverse) ++ action.event->reverse(); ++ else ++ action.event->execute(); ++ } ++ } ++}; ++ + QAbstractAnimationJob* QQuickParentAnimation::transition(QQuickStateActions &actions, + QQmlProperties &modified, + TransitionDirection direction, +@@ -207,26 +228,6 @@ + { + Q_D(QQuickParentAnimation); + +- struct QQuickParentAnimationData : public QAbstractAnimationAction +- { +- QQuickParentAnimationData() : reverse(false) {} +- ~QQuickParentAnimationData() { qDeleteAll(pc); } +- +- QQuickStateActions actions; +- //### reverse should probably apply on a per-action basis +- bool reverse; +- QList pc; +- void doAction() Q_DECL_OVERRIDE +- { +- for (int ii = 0; ii < actions.count(); ++ii) { +- const QQuickStateAction &action = actions.at(ii); +- if (reverse) +- action.event->reverse(); +- else +- action.event->execute(); +- } +- } +- }; + + QQuickParentAnimationData *data = new QQuickParentAnimationData; + QQuickParentAnimationData *viaData = new QQuickParentAnimationData; -- GitLab From d317cb36e4f485d2c085ec479c273cb0401d92f1 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Mon, 29 Aug 2016 12:16:03 +0000 Subject: [PATCH 281/701] {lib}[foss/2016a] pandas v0.18.0 For both version 2.7.x and 3.5.x version of python --- .../pandas-0.18.0-foss-2016a-Python-2.7.11.eb | 23 +++++++++++++++++++ .../pandas-0.18.0-foss-2016a-Python-3.5.1.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..9fd43e27cf --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..a23b70abda --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 90f7c9b02ca64e3c6fd40b06d60174ca0ee8b1c4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 29 Aug 2016 16:09:10 +0200 Subject: [PATCH 282/701] Add libxml2 with Python support --- ...libxml2-2.9.4-intel-2016b-Python-2.7.12.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..31fcc636e9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +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': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB --with-python=$EBROOTPYTHON/bin/python --with-python-install-dir=%(installdir)s/lib/python%(pyshortver)s/site-packages' + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), +] + + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' -- GitLab From ffb61973f79d4d09619d6af366feed0bd583100e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Aug 2016 17:39:40 +0200 Subject: [PATCH 283/701] add tcsh as OS dep in NAMD easyconfigs --- .../easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-ibverbs.eb | 6 +++++- easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-mpi.eb | 6 +++++- .../easyconfigs/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb | 6 +++++- .../easyconfigs/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb | 6 +++++- .../easyconfigs/n/NAMD/NAMD-2.9-goolf-1.4.10-ibverbs.eb | 6 +++++- .../easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-ibverbs.eb | 6 +++++- easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-mpi.eb | 6 +++++- 7 files changed, 35 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-ibverbs.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-ibverbs.eb index ca09534948..007dda5df8 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-ibverbs.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.10b1' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'pic': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-mpi.eb index 8c61d5ae85..cb852fe76d 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-mpi.eb @@ -3,7 +3,8 @@ version = '2.10b1' versionsuffix = '-mpi' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = 'mpi-linux-x86_64' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb index e2998dd325..35ee273440 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'gmvapich2', 'version': '1.7.12'} toolchainopts = {'opt': True, 'pic': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb index 9434c5a602..c1bef55488 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} toolchainopts = {'opt': True, 'pic': True} @@ -14,6 +15,9 @@ dependencies = [ ('Tcl', '8.5.12'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-goolf-1.4.10-ibverbs.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-goolf-1.4.10-ibverbs.eb index 1bbb708c5e..b2ccba3358 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-goolf-1.4.10-ibverbs.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-goolf-1.4.10-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True} @@ -14,6 +15,9 @@ dependencies = [ ('Tcl', '8.5.12'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-ibverbs.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-ibverbs.eb index b18bbca8a4..05806930d2 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-ibverbs.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'pic': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-mpi.eb index 2fbdf05529..427a25848b 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-mpi.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-mpi' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = 'mpi-linux-x86_64' moduleclass = 'chem' -- GitLab From ffbfdb90cbeefdad963e959ac3461fe3da0349b0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Aug 2016 22:15:31 +0100 Subject: [PATCH 284/701] add easyconfig HISAT2-2.0.4-foss-2016b.eb --- .../h/HISAT2/HISAT2-2.0.4-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb new file mode 100644 index 0000000000..354eb721c4 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.4' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +checksums = ['50119a693929e240b072d79e69dc211e'] + +dependencies = [ + ('NGS', '1.2.3'), + ('ncbi-vdb', '2.5.8-1'), +] + +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c3c1e5597345833cedbe3224c18be74684624b6c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Aug 2016 22:19:41 +0100 Subject: [PATCH 285/701] add easyconfig Clustal-Omega-1.2.0-foss-2016b.eb --- .../Clustal-Omega-1.2.0-foss-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb new file mode 100644 index 0000000000..06226cf0b0 --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.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 +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.0' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 8627a5042f877779341b73d43501f7aef1ce79ae Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Aug 2016 22:26:54 +0100 Subject: [PATCH 286/701] add easyconfig cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb --- ...cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..63398f9cb0 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.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 (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cutadapt/'], +} + +moduleclass = 'bio' -- GitLab From f8f47c8da1f110134e465bf7cb787cd123966a11 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 29 Aug 2016 22:34:27 +0100 Subject: [PATCH 287/701] add easyconfig GATK-3.6-Java-1.8.0_92.eb --- .../g/GATK/GATK-3.6-Java-1.8.0_92.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb new file mode 100644 index 0000000000..3bbed9824e --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , 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 +# Modified by: Adam Huffman +# The Francis Crick Institute +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '3.6' +versionsuffix = '-Java-%(javaver)s' + +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 = ['GenomeAnalysisTK-%(version)s.tar.bz2'] + +dependencies = [('Java', '1.8.0_92')] + +modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' -- GitLab From 7681cae021e90136d0c24069aff74d3bbbd73a1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Aug 2016 08:43:54 +0200 Subject: [PATCH 288/701] add easyconfig worker-1.6.6-intel-2016b.eb --- .../w/worker/worker-1.6.6-intel-2016b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.6-intel-2016b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.6-intel-2016b.eb new file mode 100644 index 0000000000..dd9436b448 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.6-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.6' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.24.0') +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2016b@g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', +] + +moduleclass = 'tools' -- GitLab From a2e19cfcbe69c5372256232590200e0879f9d301 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 30 Aug 2016 10:19:09 +0200 Subject: [PATCH 289/701] move lrt flag inside comments --- .../easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb index 140e2b5ff8..7988df3582 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb @@ -29,6 +29,6 @@ dependencies = [ builddependencies = [('CMake', '3.5.2')] -configopts = '--LIBS="$LIBS" -lrt' +configopts = '--LIBS="$LIBS -lrt"' moduleclass = 'numlib' -- GitLab From 3dbff11d8b025de4df106f5ba4cd899e0afa0036 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 30 Aug 2016 10:03:52 +0100 Subject: [PATCH 290/701] Add missing deps NGS-1.2.3 and ncbi-vdb-2.5.8-1 --- .../easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb | 35 +++++++++++++++++ .../n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb | 38 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb new file mode 100644 index 0000000000..5ebb8f01ff --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.2.3' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_92', '', True)] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb new file mode 100644 index 0000000000..d6359bf739 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.5.8-1' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('file', '5.25'), # provides libmagic + ('HDF5', '1.8.17'), + ('NGS', '1.2.3'), +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 56e577af17e733ab2cc9fc4e498246a7470c5c0b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 30 Aug 2016 10:08:16 +0100 Subject: [PATCH 291/701] Add missing dep argtable-2.13 --- .../a/argtable/argtable-2.13-foss-2016b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb new file mode 100644 index 0000000000..7323bc0d88 --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb @@ -0,0 +1,27 @@ +i# 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: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'argtable' +version = '2.13' + +homepage = 'http://argtable.sourceforge.net/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] + +sanity_check_paths = { + 'files': ['lib/libargtable2.so', 'lib/libargtable2.la'], + 'dirs': ['include', 'lib', 'share'], +} + +moduleclass = 'lib' -- GitLab From 2cb810130cd4e6f180710734421bb8bc366f1cb8 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 30 Aug 2016 11:25:13 +0200 Subject: [PATCH 292/701] use sed to remove hardcoded CC in makefile --- .../easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch deleted file mode 100644 index 7bd94606e9..0000000000 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4_CC.patch +++ /dev/null @@ -1,13 +0,0 @@ -#Subtitue hardcoded cc for gcc to prevent 'cc1: error: unrecognized command line option "-fstack-protector-strong"' -#Author: Ruben van Dijk (University of Groningen) ---- bio-tools-psort-all/bio-tools-psort-modhmm/Makefile 2016-08-29 09:40:30.000000000 +0200 -+++ bio-tools-psort-all/bio-tools-psort-modhmm/Makefile 2016-08-29 09:40:14.000000000 +0200 -@@ -34,7 +34,7 @@ - # These definitions are from config.sh (via /software/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/Config.pm). - # They may have been overridden via Makefile.PL or on the command line. - AR = ar --CC = cc -+CC ?= gcc - CCCDLFLAGS = -fPIC - CCDLFLAGS = -Wl,-E - DLEXT = so -- GitLab From 64c793b5e792458e6a20d3735697687e22d43538 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 30 Aug 2016 11:28:26 +0200 Subject: [PATCH 293/701] Use sed for hardcoded CC and removed patch --- .../p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index 6da5f456df..79449c632c 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -14,7 +14,6 @@ sources = ['bio-tools-psort-all.%(version)s.tar.gz'] patches = [ 'PSORTb-%(version)s-libpsortb.patch', - 'PSORTb-%(version)s_CC.patch', ] dependencies = [ @@ -29,6 +28,8 @@ options = {'modulename': 'Bio::Tools::PSort'} preconfigopts = "export PSORTROOT=%(installdir)s && " +prebuildopts = 'sed -i "s/CC = cc/CC ?= gcc/" bio-tools-psort-modhmm/Makefile && ' + postinstallcmds = [ "cp -r psort/* %(installdir)s/.", ] -- GitLab From a417e70714d2edaef0b347e6d756a6063b283fd3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 30 Aug 2016 10:51:52 +0100 Subject: [PATCH 294/701] Fix vim-related typo --- easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb index 7323bc0d88..ec3422f109 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb @@ -1,4 +1,4 @@ -i# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# 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 -- GitLab From ac3369681848e21bade5e1b8471c53b8d2084024 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 30 Aug 2016 10:54:38 +0100 Subject: [PATCH 295/701] Add missing dep file, updated to latest upstream --- .../f/file/file-5.28-foss-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb b/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb new file mode 100644 index 0000000000..51d81cd710 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.28' + +homepage = 'http://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' -- GitLab From c3440d6ca2ec7dd03a2e1730e877214212034e22 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 30 Aug 2016 13:00:11 +0200 Subject: [PATCH 296/701] Added foss 2016a version of GObject-Introspection, which was missing. This version is based on the intel 2016a one. --- ...GObject-Introspection-1.48.0-foss-2016a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb new file mode 100644 index 0000000000..e8ddb76e89 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.48.0' + +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': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('Python', '2.7.11'), + ('GLib', glibver), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6', '-GLib-%s' % glibver), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +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'] +} + +moduleclass = 'devel' -- GitLab From 4d15c07c27f76c3097df8c8273f16fda020017a3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 30 Aug 2016 12:18:56 +0100 Subject: [PATCH 297/701] Make sure ncbi-vdb picks up newest version of file dep --- easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb index d6359bf739..e0bd19a121 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.5.8-1-foss-2016b.eb @@ -14,7 +14,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('libxml2', '2.9.4'), - ('file', '5.25'), # provides libmagic + ('file', '5.28'), # provides libmagic ('HDF5', '1.8.17'), ('NGS', '1.2.3'), ] -- GitLab From 6840cb1e8862aecd98fc1dab44bffada22c08dcf Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 30 Aug 2016 13:41:26 +0200 Subject: [PATCH 298/701] Version of cairo built using the foss 2016a toolchain. --- .../cairo-1.14.6-foss-2016a-GLib-2.48.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000..9259854841 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' +glibver = '2.48.0' +versionsuffix = '-GLib-%s' % glibver + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.3'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.95'), + ('expat', '2.1.1'), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), + ('GLib', glibver), +] +builddependencies = [ + ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 7c6da77cb29676336de4a88816a4344b75884469 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 30 Aug 2016 13:58:34 +0200 Subject: [PATCH 299/701] Javaversion lines dropped --- easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb index 1b99713c8c..58018d9335 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb @@ -25,12 +25,9 @@ builddependencies = [ ('Autotools', '20150215'), ] -java = 'Java' -javaver = '1.8.0_92' - dependencies = [ ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-%s-%s' % (java, javaver), True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.8'), ('ncurses', '6.0',), -- GitLab From 0b2dec1d8fbe1b43c98f0be38ee5418f6066ad0d Mon Sep 17 00:00:00 2001 From: jhein32 Date: Tue, 30 Aug 2016 14:04:09 +0200 Subject: [PATCH 300/701] renamed to v 2016.07, cleanup of imkl e-conf --- ...l-2016.03b.eb => HPL-2.1-iomkl-2016.07.eb} | 2 +- .../i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb | 19 ---------- .../i/imkl/imkl-11.3.3.210-iompi-2016.07.eb | 36 +++++++++++++++++++ .../{iomkl-2016.03b.eb => iomkl-2016.07.eb} | 2 +- .../{iompi-2016.03b.eb => iompi-2016.07.eb} | 2 +- ...0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 4 --- 6 files changed, 39 insertions(+), 26 deletions(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.1-iomkl-2016.03b.eb => HPL-2.1-iomkl-2016.07.eb} (92%) delete mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb rename easybuild/easyconfigs/i/iomkl/{iomkl-2016.03b.eb => iomkl-2016.07.eb} (96%) rename easybuild/easyconfigs/i/iompi/{iompi-2016.03b.eb => iompi-2016.07.eb} (95%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.03b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb similarity index 92% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.03b.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb index ffef7bda94..42249afb29 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.03b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.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': 'iomkl', 'version': '2016.03b'} +toolchain = {'name': 'iomkl', 'version': '2016.07'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb deleted file mode 100644 index b1e79f9023..0000000000 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.03b.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'imkl' -version = '11.3.3.210' - -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': 'iompi', 'version': '2016.03b'} - -sources = ['l_mkl_%(version)s.tgz'] - -dontcreateinstalldir = '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/imkl/imkl-11.3.3.210-iompi-2016.07.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb new file mode 100644 index 0000000000..e0337a09f8 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb @@ -0,0 +1,36 @@ +name = 'imkl' +version = '11.3.3.210' + +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': 'iompi', 'version': '2016.07'} + +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +interfaces = True + +license_file = HOME + '/licenses/intel/license.lic' + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.03b.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb similarity index 96% rename from easybuild/easyconfigs/i/iomkl/iomkl-2016.03b.eb rename to easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb index 5d9f057934..54ed73649a 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.03b.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'iomkl' -version = '2016.03b' +version = '2016.07' 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.""" diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.03b.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.07.eb similarity index 95% rename from easybuild/easyconfigs/i/iompi/iompi-2016.03b.eb rename to easybuild/easyconfigs/i/iompi/iompi-2016.07.eb index 7643f45613..6cfe2ee825 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.03b.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.07.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'iompi' -version = '2016.03b' +version = '2016.07' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index 377f0bee91..fb308c3df3 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -15,10 +15,6 @@ toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] -# builddependencies = [('Autotools', '20150215', '', ('GCC', '5.4.0-2.26'))] - -# preconfigopts = './autogen.sh && ' - sanity_check_paths = { 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], 'dirs': ['share/man', 'include'] -- GitLab From acd9d84f47495dc83680e8c7014f886967d85d26 Mon Sep 17 00:00:00 2001 From: jhein32 Date: Tue, 30 Aug 2016 14:15:49 +0200 Subject: [PATCH 301/701] stylistic change --- easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb index e0337a09f8..425ca0043d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb @@ -8,9 +8,8 @@ BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, a toolchain = {'name': 'iompi', 'version': '2016.07'} -checksums = ['f72546df27f5ebb0941b5d21fd804e34'] - sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] dontcreateinstalldir = 'True' -- GitLab From f5e234d48da2a6dc3a5c156bf0639a101f31c907 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 30 Aug 2016 15:06:02 +0200 Subject: [PATCH 302/701] Migrate-N with foss2016a --- .../m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb | 42 +++++++++++++++++++ .../m/MIGRATE-N/migrate-4.2.8_install.patch | 13 ++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.8_install.patch diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb new file mode 100644 index 0000000000..b6f05aeb5d --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'MIGRATE-N' +version = '4.2.8' + +homepage = 'http://popgen.sc.fsu.edu/Migrate/Migrate-n.html' +description = """ +Migrate estimates population parameters, effective population sizes +and migration rates of n populations, using genetic data. It +uses a coalescent theory approach taking into account history of +mutations and uncertainty of the genealogy. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['migrate-%(version)s.src.tar.gz'] +source_urls = [ + 'http://popgen.sc.fsu.edu/currentversions/', + 'http://popgen.sc.fsu.edu/oldversions/%(version_major)s.x/%(version_major_minor)s', + 'http://popgen.sc.fsu.edu/oldversions/', + 'http://popgen.sc.fsu.edu/newversions/', +] + +patches = [ + 'migrate-%(version)s_install.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-A4 "CC=$CC" STDCPLUS=-lstdc++ ' +prebuildopts = 'make mpis && make clean && ' + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['migrate-n','migrate-n-mpi']], + 'dirs': ['man'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.8_install.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.8_install.patch new file mode 100644 index 0000000000..97957ab44e --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.8_install.patch @@ -0,0 +1,13 @@ +#Create parent directories during install +#B. Hajgato January 18th, 2016 +--- src/configure.orig 2014-12-28 03:46:09.000000000 +0100 ++++ src/configure 2016-01-18 14:57:26.331047715 +0100 +@@ -3411,7 +3411,7 @@ + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then +- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" ++ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c -D" + break 3 + fi + fi -- GitLab From d8618a889b46f1dea4314300b8fc63e77e53e27e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 30 Aug 2016 16:29:58 +0200 Subject: [PATCH 303/701] without optarch --- .../o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb index 1aafb42367..8d4c77f654 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,7 @@ description = """Open Babel is a chemical toolbox designed to speak the many solid-state materials, biochemistry, or related areas.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'strict': True} +toolchainopts = {'strict': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 8b3d55a39d70efddcfb0ae814eca2df1a6ec49e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2016 08:59:19 +0200 Subject: [PATCH 304/701] add easyconfig matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb, add easyconfig matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb --- ...plotlib-1.5.1-intel-2016b-Python-2.7.12.eb | 2 +- ...plotlib-1.5.2-intel-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 2 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb index 32e0314072..633cf0c29a 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb @@ -27,7 +27,7 @@ exts_list = [ 'source_tmpl': 'cycler-%(version)s.tar.gz', }), (name, version, { - 'source_urls': [PYPI_SOURCE], + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], }), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..b85eaba8bb --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.2' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('freetype', '2.6.5'), + ('libpng', '1.6.24'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# 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': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From 231364cfd73599b6a976fe92410c9fba000a1c09 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 31 Aug 2016 13:06:55 +0200 Subject: [PATCH 305/701] Make binutils a dep instead of a buidldep... since we have a bin directory --- easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb index a702a8acce..3e0ed4ee14 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb @@ -18,13 +18,13 @@ source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ - ('binutils', '2.25'), ('CMake', '3.6.1'), # We use the minimal Python in GCCcore ('Python', '2.7.12', '-bare'), ] dependencies = [ + ('binutils', '2.25'), # Has executables so needs an explicit binutils dep ('ncurses', '6.0'), ] -- GitLab From 81c0bc48cd760db273e8b6655253d018ee634a03 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 31 Aug 2016 13:20:58 +0200 Subject: [PATCH 306/701] Missed a very important space --- easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb index 3e0ed4ee14..af227cc9f2 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb @@ -28,7 +28,7 @@ dependencies = [ ('ncurses', '6.0'), ] -configopts = '-DBUILD_SHARED_LIBS=ON' +configopts = '-DBUILD_SHARED_LIBS=ON ' # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON" -- GitLab From 277daf5e5593bc16083c34be5968a91784b2cb09 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 31 Aug 2016 13:22:21 +0200 Subject: [PATCH 307/701] Put binutils back as a builddep only --- easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb index af227cc9f2..fe4a09d2cd 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb @@ -18,13 +18,13 @@ source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ + ('binutils', '2.25'), ('CMake', '3.6.1'), # We use the minimal Python in GCCcore ('Python', '2.7.12', '-bare'), ] dependencies = [ - ('binutils', '2.25'), # Has executables so needs an explicit binutils dep ('ncurses', '6.0'), ] -- GitLab From 87634784a7de600239154f381e3d6c2813a8022d Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 31 Aug 2016 13:24:17 +0200 Subject: [PATCH 308/701] Binutils is builddep only --- .../easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index c12401c785..62cd674cc5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -11,8 +11,11 @@ toolchainopts = {'pic': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -dependencies = [ +builddependencies = [ ('binutils', '2.25'), +] + +dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('libreadline', '6.3'), -- GitLab From a3775826c5122907372b15fd6556cf8c28aac614 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2016 13:28:48 +0200 Subject: [PATCH 309/701] add missing 'easyblock' specs & update unfinished HEALPix easyconfig (but still WIP) --- .../easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb | 8 +++++--- .../c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb | 6 ++++-- .../easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb | 10 ++++------ .../c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb | 10 ++++++---- .../easyconfigs/c/CRPropa/CRPropa_no-docs.patch | 11 ----------- .../h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb | 12 ++++++++++++ 6 files changed, 31 insertions(+), 26 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb index 1c5fae9cf7..152bd6207a 100755 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'Bison' version = '3.0.1' @@ -8,13 +10,13 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +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':[], + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb index 3653e27ca4..177bb20dcc 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'CFITSIO' version = '3.350' @@ -13,8 +15,8 @@ source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { - 'files':["lib/libcfitsio.a"], - 'dirs':["include"], + 'files': ["lib/libcfitsio.a"], + 'dirs': ["include"], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb index 09d2be584e..380b94f6c7 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb @@ -11,15 +11,13 @@ description = """The CLHEP project is intended to be a set of HEP-specific found toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] builddependencies = [('CMake', '2.8.12')] -# CLHEP compiles with icc instead of icpc, required out-of-source dir -srcdir = "../CLHEP" -preconfigopts = 'cd .. && mkdir obj && cd obj && export CXX="$CC" && ' -premakeopts = 'cd ../obj &&' -preinstallopts = 'cd ../obj &&' +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb index 627472338f..7d9e835291 100644 --- a/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'CRPropa' version = '2.0.3' @@ -7,10 +9,10 @@ description = """CRPropa is a publicly available code to study the propagation o toolchain = {'name': 'ictce', 'version': '5.5.0'} -# download from https://github.com/CRPropa/CRPropa2 -sources = ['%(name)s%(version_major)s-%(version)s.tar.gz'] +source_urls = ['https://github.com/CRPropa/CRPropa2/archive/'] +sources = ['v%(version)s.tar.gz'] -patches = ['CRPropa_no-docs.patch'] +patches = ['CRPropa-%(version)s_no-docs.patch'] dependencies = [ ('CLHEP', '2.1.3.1'), @@ -25,7 +27,7 @@ configopts += '--with-cfitsio-include=$EBROOTCFITSIO/include --with-cfitsio-libr configopts += '--with-root=$EBROOTROOT/lib' # download and install the photo disintegration data package -premakeopts = './GetPDCrossSections.sh && ' +prebuildopts = './GetPDCrossSections.sh && ' runtest = 'check' diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch b/easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch deleted file mode 100644 index f422512b07..0000000000 --- a/easybuild/easyconfigs/c/CRPropa/CRPropa_no-docs.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- Makefile.in.orig 2014-03-26 17:18:53.474997093 +0100 -+++ Makefile.in 2014-03-26 17:19:18.844596386 +0100 -@@ -291,7 +291,7 @@ - AM_CPPFLAGS = $(GNL_CPPFLAGS) - - #SUBDIRS = External doc sophia dint src --SUBDIRS = External sophia sibyll dint src doc -+SUBDIRS = External sophia sibyll dint src # doc - EXTRA_DIST = sophia/src/sophia.h sibyll/sibyll.h src/Interactions/proton_f77 src/Interactions/proton_sophia dint/src/tables sysdep.h get_externals.sh GetPDCrossSections.sh HalfLifeTable doc/Doxyfile COPYRIGHT doc/UserGuide.tex doc/precision_traj.ps doc/PhotonDensityCollection2.eps doc/crpdetector.eps doc/AllIRBzEvolutionModelsCan.eps IRBzRedshiftEvol_Kneiske examples/GettingStarted Plot - all: config.h - $(MAKE) $(AM_MAKEFLAGS) all-recursive diff --git a/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb index 597c5e6d42..eaa845a70c 100644 --- a/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'HEALPix' version = '2.20a' @@ -12,4 +14,14 @@ sources = ['Healpix_%(version)s_2011Feb09.tar.gz'] dependencies = [('CFITSIO', '3.350')] +buildininstalldir = True + +skipsteps = ['configure'] +prebuildopts = "./configure -L && " + +sanity_check_paths = { + 'files': [], + 'dirs': [], +} + moduleclass = 'math' -- GitLab From 999c230a375dc71fa048b3b22aa679af6d62f627 Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 31 Aug 2016 13:46:22 +0200 Subject: [PATCH 310/701] Keep using system python though jhbuild can be used with any python2 if it is leveraged during a build process --- .../easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb index 9186755910..2ee0addc3e 100644 --- a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -15,12 +15,13 @@ source_urls = [('https://github.com/GNOME/jhbuild/archive/')] # jhbuild is python so it has a python dependency, but we want to give people freedom to use whatever python they # chose during a build process +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + builddependencies = [ - ('Python', '2.7.12', '-bare'), + ('binutils', '2.25'), ] dependencies = [ - ('binutils', '2.25'), ('Autotools', '20150215'), ('pkg-config', '0.29.1'), ('gettext', '0.19.8'), @@ -44,4 +45,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'lib' -- GitLab From 2b457fdebfe9febf1b1d981ea9ef602b375bd759 Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 31 Aug 2016 13:48:40 +0200 Subject: [PATCH 311/701] Change category to tools --- .../easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb index 2ee0addc3e..edb6e68f45 100644 --- a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -45,4 +45,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'lib' +moduleclass = 'tools' -- GitLab From 49362eace58ce38b791c0f2d21cf38e2fd79af49 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 31 Aug 2016 13:50:54 +0200 Subject: [PATCH 312/701] Delete Python-2.7.12-GCCcore-4.9.3-bare.eb --- .../Python-2.7.12-GCCcore-4.9.3-bare.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb deleted file mode 100644 index be62c66c15..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'Python' -version = '2.7.12' -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': 'GCCcore', 'version': '4.9.3'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -dependencies = [ - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '6.0'), - ('SQLite', '3.14.1'), - # ('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')] - -# We hide this by default since users should not use it in production -#hidden = True - -# bare installation: only known module deps for GCCcore tools included -exts_list =[] - -moduleclass = 'lang' -- GitLab From aaf3e7fc4c811750d18cc56d81033d23cd19d3b5 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 31 Aug 2016 13:51:27 +0200 Subject: [PATCH 313/701] Delete SQLite-3.14.1-GCCcore-4.9.3.eb --- .../s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb deleted file mode 100644 index d38cf61101..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb +++ /dev/null @@ -1,44 +0,0 @@ -## -# 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 = '3.14.1' - -homepage = 'http://www.sqlite.org/' -description = 'SQLite: SQL Database Engine in a C Library' - -toolchain = {'name': 'GCCcore', 'version': '4.9.3'} - -# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz -source_urls = ['http://www.sqlite.org/2016/'] -version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) -sources = ['sqlite-autoconf-%s.tar.gz' % version_str] - -builddependencies = [ - ('binutils', '2.25'), -] - -dependencies = [ - ('libreadline', '6.3'), - ('Tcl', '8.6.6'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'devel' -- GitLab From 3212b9019d609890bc1843b2138e3e360e8948ee Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 31 Aug 2016 13:51:50 +0200 Subject: [PATCH 314/701] Delete Tcl-8.6.6-GCCcore-4.9.3.eb --- .../t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb deleted file mode 100644 index 35b772ac6f..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.6' - -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': 'GCCcore', 'version': '4.9.3'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -builddependencies = [ - ('binutils', '2.25'), -] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' -- GitLab From f2124c8361243215f760d406fba5652c35f10a51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2016 14:40:11 +0200 Subject: [PATCH 315/701] revert back changes to HEALPix, since it requires a custom easyblock --- .../h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb index eaa845a70c..597c5e6d42 100644 --- a/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'HEALPix' version = '2.20a' @@ -14,14 +12,4 @@ sources = ['Healpix_%(version)s_2011Feb09.tar.gz'] dependencies = [('CFITSIO', '3.350')] -buildininstalldir = True - -skipsteps = ['configure'] -prebuildopts = "./configure -L && " - -sanity_check_paths = { - 'files': [], - 'dirs': [], -} - moduleclass = 'math' -- GitLab From c5f4789bd76c28d2c91a15a1aeec3d3ce7cf90b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2016 15:47:03 +0200 Subject: [PATCH 316/701] fix source URLs for Perl extensions --- .../p/Perl/Perl-5.16.3-ictce-5.5.0.eb | 106 +++++++++--------- 1 file changed, 53 insertions(+), 53 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb index 106bbda74e..6d7b68ab45 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb @@ -17,208 +17,208 @@ runtest = 'test' exts_list = [ ('IO::String', '1.08', { 'source_tmpl': 'IO-String-1.08.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/IO/GAAS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('Data::Stag', '0.11', { 'source_tmpl': 'Data-Stag-0.11.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Data/CMUNGALL/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], }), ('DB_File', '1.827', { - 'source_urls': ['http://www.cpan.org/modules/by-module/DB_File/PMQS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PM/PMQS/'], }), ('DBI', '1.625', { - 'source_urls': ['http://www.cpan.org/modules/by-module/DBI/TIMB/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TI/TIMB/'], }), ('Bio::Perl', '1.6.901', { 'source_tmpl': 'BioPerl-1.6.901.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], 'patches': ['BioPerl_disable-broken-test.patch'], }), ('Sub::Uplevel', '0.24', { 'source_tmpl': 'Sub-Uplevel-0.24.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/DAGOLDEN/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], }), ('Tree::DAG_Node', '1.11', { 'source_tmpl': 'Tree-DAG_Node-1.11.tgz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Tree/RSAVAGE/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], }), ('Try::Tiny', '0.12', { 'source_tmpl': 'Try-Tiny-0.12.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Test::Fatal', '0.010', { 'source_tmpl': 'Test-Fatal-0.010.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/RJBS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Test::Exception', '0.31', { 'source_tmpl': 'Test-Exception-0.31.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/ADIE/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADIE/'], }), ('Test::Warn', '0.24', { 'source_tmpl': 'Test-Warn-0.24.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/CHORNY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], }), ('Test::Requires', '0.06', { 'source_tmpl': 'Test-Requires-0.06.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/TOKUHIROM/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM/'], }), ('Test::Tester', '0.108', { 'source_tmpl': 'Test-Tester-0.108.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/FDALY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FD/FDALY/'], }), ('Params::Util', '1.07', { 'source_tmpl': 'Params-Util-1.07.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Params/ADAMK/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Sub::Install', '0.926', { 'source_tmpl': 'Sub-Install-0.926.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Data::OptList', '0.107', { 'source_tmpl': 'Data-OptList-0.107.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Data/RJBS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Sub::Exporter', '0.985', { 'source_tmpl': 'Sub-Exporter-0.985.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Test::Output', '1.01', { 'source_tmpl': 'Test-Output-1.01.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/BDFOY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], }), ('Module::Runtime', '0.013', { 'source_tmpl': 'Module-Runtime-0.013.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Module/ZEFRAM/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/'], }), ('Module::Implementation', '0.06', { 'source_tmpl': 'Module-Implementation-0.06.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Module/DROLSKY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('List::MoreUtils', '0.33', { 'source_tmpl': 'List-MoreUtils-0.33.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/List/ADAMK/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Package::DeprecationManager', '0.13', { 'source_tmpl': 'Package-DeprecationManager-0.13.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DROLSKY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Dist::CheckConflicts', '0.02', { 'source_tmpl': 'Dist-CheckConflicts-0.02.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Dist/DOY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Package::Stash', '0.34', { 'source_tmpl': 'Package-Stash-0.34.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DOY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Class::Load', '0.20', { 'source_tmpl': 'Class-Load-0.20.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Class/DROLSKY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('MRO::Compat', '0.12', { 'source_tmpl': 'MRO-Compat-0.12.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BO/BOBTFISH/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH/'], }), ('Sub::Name', '0.05', { 'source_tmpl': 'Sub-Name-0.05.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/FLORA/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FL/FLORA/'], }), ('Eval::Closure', '0.08', { 'source_tmpl': 'Eval-Closure-0.08.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Sub::Exporter::Progressive', '0.001010', { 'source_tmpl': 'Sub-Exporter-Progressive-0.001010.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/FREW/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW/'], }), ('Devel::GlobalDestruction', '0.11', { 'source_tmpl': 'Devel-GlobalDestruction-0.11.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Devel/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], }), ('boolean', '0.30', { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IN/INGY/'], }), ('Tie::IxHash', '1.23', { 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Tie/CHORNY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], }), ('Moose', '2.0801', { - 'source_urls': ['http://www.cpan.org/modules/by-module/MooseX/ETHER/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Params::Validate', '1.07', { 'source_tmpl': 'Params-Validate-1.07.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Params/DROLSKY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('DateTime::Locale', '0.45', { 'source_tmpl': 'DateTime-Locale-0.45.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Class::Singleton', '1.4', { 'source_tmpl': 'Class-Singleton-1.4.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Class/ABW/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], }), ('DateTime::TimeZone', '1.58', { 'source_tmpl': 'DateTime-TimeZone-1.58.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('DateTime', '1.01', { - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Data::Types', '0.09', { 'source_tmpl': 'Data-Types-0.09.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Data/DWHEELER/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], }), ('DateTime::Tiny', '1.04', { 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/ADAMK/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('File::Slurp', '9999.19', { 'source_tmpl': 'File-Slurp-9999.19.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/File/URI/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI/'], }), ('HTTP::Date', '6.02', { 'source_tmpl': 'HTTP-Date-6.02.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/HTTP/GAAS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('IO::HTML', '1.00', { 'source_tmpl': 'IO-HTML-1.00.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/IO/CJM/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM/'], }), ('LWP::MediaTypes', '6.02', { 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/LWP/GAAS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('URI', '1.60', { - 'source_urls': ['http://www.cpan.org/modules/by-module/URI/GAAS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTTP::Request', '6.06', { 'source_tmpl': 'HTTP-Message-6.06.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/HTTP/GAAS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTML::Tagset', '3.20', { 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/HTML/PETDANCE/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], }), ('HTML::Entities', '3.70', { 'source_tmpl': 'HTML-Parser-3.70.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/HTML/GAAS/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('AnyEvent', '7.04', { - 'source_urls': ['http://www.cpan.org/modules/by-module/AnyEvent/MLEHMANN/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], }), ('Mouse', '1.05', { - 'source_urls': ['http://www.cpan.org/modules/by-module/MouseX/GFUJI/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], }), ('XML::NamespaceSupport', '1.11', { 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/XML/PERIGRIN/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], }), ('XML::SAX::Base', '1.08', { 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/XML/GRANTM/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], }), ('XML::SAX', '0.99', { 'source_tmpl': 'XML-SAX-0.99.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/XML/GRANTM/'], + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], }), ] -- GitLab From 817470698f41c0098df121e14e453edf8df96de8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2016 15:48:36 +0200 Subject: [PATCH 317/701] add missing patch file for CRPropa --- .../c/CRPropa/CRPropa-2.0.3_no-docs.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3_no-docs.patch diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3_no-docs.patch b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3_no-docs.patch new file mode 100644 index 0000000000..98c5588397 --- /dev/null +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3_no-docs.patch @@ -0,0 +1,13 @@ +skip building of docs +author: Kenneth Hoste (HPC-UGent) +--- Makefile.in.orig 2014-03-26 17:18:53.474997093 +0100 ++++ Makefile.in 2014-03-26 17:19:18.844596386 +0100 +@@ -291,7 +291,7 @@ + AM_CPPFLAGS = $(GNL_CPPFLAGS) + + #SUBDIRS = External doc sophia dint src +-SUBDIRS = External sophia sibyll dint src doc ++SUBDIRS = External sophia sibyll dint src # doc + EXTRA_DIST = sophia/src/sophia.h sibyll/sibyll.h src/Interactions/proton_f77 src/Interactions/proton_sophia dint/src/tables sysdep.h get_externals.sh GetPDCrossSections.sh HalfLifeTable doc/Doxyfile COPYRIGHT doc/UserGuide.tex doc/precision_traj.ps doc/PhotonDensityCollection2.eps doc/crpdetector.eps doc/AllIRBzEvolutionModelsCan.eps IRBzRedshiftEvol_Kneiske examples/GettingStarted Plot + all: config.h + $(MAKE) $(AM_MAKEFLAGS) all-recursive -- GitLab From a340a32f731448eb954f1467559c06ca1ef6ab9e Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 31 Aug 2016 17:03:26 +0200 Subject: [PATCH 318/701] Add CVS dependency --- .../c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb | 30 +++++++++++++++++++ .../jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 1 + 2 files changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..e9bbed8bb4 --- /dev/null +++ b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'CVS' +version = '1.11.23' + +homepage = 'https://savannah.nongnu.org/projects/cvs' +description = """CVS is a version control system, an important component of + Source Configuration Management (SCM).""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['CVS-1.11.23-zlib-1.patch', 'CVS-1.11.23-getline.patch'] + +builddependencies = [('binutils', '2.25')] +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ['bin/cvs', 'bin/cvsbug', 'bin/rcs2log'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb index edb6e68f45..b2f1cf65eb 100644 --- a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -28,6 +28,7 @@ dependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), ('M4', '1.4.17'), + ('CVS', '1.11.23'), ] # We use the simple install method as per: -- GitLab From cfc92cac078a292f032d0dce8f1487005abe4d4a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 31 Aug 2016 17:35:29 +0200 Subject: [PATCH 319/701] Add extra options and newer cmake for CGAL/4.8.1 The newer CMake is needed as 3.5.2 does not support the intel compiler in 2016b (no features found). --- .../easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb index e6a3b147ae..406b208a88 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb @@ -20,13 +20,15 @@ dependencies = [ ('Qt5', '5.7.0'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " -configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT - builddependencies = [ - ('CMake', '3.5.2'), + ('CMake', '3.6.1'), ('Eigen', '3.2.9'), ] +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + moduleclass = 'numlib' -- GitLab From 88b1093af056140deb4fdbeed9b569f57abe467c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 31 Aug 2016 17:50:22 +0200 Subject: [PATCH 320/701] Add CMake/3.6.1 for intel/2016b --- .../c/CMake/CMake-3.6.1-intel-2016b.eb | 33 +++++++++++++++++++ .../c/CMake/CMake-3.6.1-use-gnu11.patch | 14 ++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb new file mode 100644 index 0000000000..40d915d152 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +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': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s-use-gnu11.patch'] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # 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', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch new file mode 100644 index 0000000000..2a6ab800b5 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch @@ -0,0 +1,14 @@ +diff -ur cmake-3.6.1.orig/Modules/Compiler/Intel-C.cmake cmake-3.6.1/Modules/Compiler/Intel-C.cmake +--- cmake-3.6.1.orig/Modules/Compiler/Intel-C.cmake 2016-07-22 15:50:22.000000000 +0200 ++++ cmake-3.6.1/Modules/Compiler/Intel-C.cmake 2016-08-31 17:32:38.594401777 +0200 +@@ -15,8 +15,8 @@ + endif() + + if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 15.0.0) +- set(CMAKE_C11_STANDARD_COMPILE_OPTION "${_std}=c11") +- set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=c11") ++ set(CMAKE_C11_STANDARD_COMPILE_OPTION "${_std}=gnu11") ++ set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=gnu11") + endif() + + if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 12.1) -- GitLab From e26c670e348aff1efa376bc44b4857ed0d47c966 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2016 18:42:34 +0200 Subject: [PATCH 321/701] add easyconfig pandas-0.18.1-intel-2016b-Python-2.7.12.eb, add easyconfig pandas-0.18.1-intel-2016b-Python-3.5.2.eb --- ...pandas-0.18.1-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ .../pandas-0.18.1-intel-2016b-Python-3.5.2.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..127a463ca2 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..11324cd1bf --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 20a3545e2b9353bb9dc4dcf600f4864f78643efc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2016 18:47:04 +0200 Subject: [PATCH 322/701] add easyconfig dask-0.11.0-intel-2016b-Python-2.7.12.eb, add easyconfig dask-0.11.0-intel-2016b-Python-3.5.2.eb --- .../dask-0.11.0-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ .../dask-0.11.0-intel-2016b-Python-3.5.2.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..27c5d182f4 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.11.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..1b19e5cf38 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.11.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From 5bbe3475640a82bd8fa8bb00c77af0d535226695 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2016 19:15:28 +0200 Subject: [PATCH 323/701] clean up sources spec for gdc-client bundle easyconfig --- .../g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb index 12d6cdfcea..8bbf7589b7 100644 --- a/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb @@ -10,9 +10,6 @@ description = """The gdc-client provides several convenience functions over the toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https://github.com/NCI-GDC/gdc-client/archive/'] -sources = ['v%(version)s.tar.gz'] - # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -- GitLab From c7f57a65cc2c3ba940b38662ead885b8f49740bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2016 19:20:36 +0200 Subject: [PATCH 324/701] add sanity check command to verify that FDS build is MPI-aware --- easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb | 3 +++ easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb | 2 ++ easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb | 2 ++ easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb | 2 ++ easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb | 2 ++ 6 files changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb index cda8fd4795..f3aacd25ad 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb @@ -34,4 +34,7 @@ sanity_check_paths = { 'files': ['FDS_Compilation/fds'], 'dirs': [], } + +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb index 8092c9cddd..6addd713dc 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb @@ -35,4 +35,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' 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 0c347df7a3..aa1cadabd3 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 @@ -29,4 +29,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' 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 13b8f521af..25ed6f846a 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 @@ -29,4 +29,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb index 26071db4b5..001132efa2 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb @@ -29,4 +29,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb index 296e2d6beb..6f8589d3e9 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb @@ -33,4 +33,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' -- GitLab From 67b802a2d5fa8720f5068e20e8f7f0eb3b6ec6ce Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 Aug 2016 17:28:06 +0200 Subject: [PATCH 325/701] Added Mesa/12.0.1 for intel/2016b --- .../l/libdrm/libdrm-2.4.70-intel-2016b.eb | 24 ++++++++ .../m/Mesa/Mesa-12.0.1-intel-2016b.eb | 58 +++++++++++++++++++ .../m/Mesa/libGLU-9.0.0-intel-2016b.eb | 24 ++++++++ 3 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/Mesa/libGLU-9.0.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb new file mode 100644 index 0000000000..9fb07a2954 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.70' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb new file mode 100644 index 0000000000..c6932e7252 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '12.0.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), +] + +dependencies = [ + ('libxml2', '2.9.4'), + ('X11', '20160819'), + ('libdrm', '2.4.70'), + ('LLVM', '3.8.1'), +# ('eudev', '3.1.5'), +] + +# Use the os provided libudev or the EB provided eudev +osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +#preconfigopts = ' libtoolize && ' + +#prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" CFLAGS= ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/libGLU-9.0.0-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/libGLU-9.0.0-intel-2016b.eb new file mode 100644 index 0000000000..1bfa6744b9 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/libGLU-9.0.0-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '12.0.1'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 5587af5083c1ee438943958a4fb3bcfbcf93bb3b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 Aug 2016 17:49:03 +0200 Subject: [PATCH 326/701] Fix easyconfig location --- .../easyconfigs/{m/Mesa => l/libGLU}/libGLU-9.0.0-intel-2016b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{m/Mesa => l/libGLU}/libGLU-9.0.0-intel-2016b.eb (100%) diff --git a/easybuild/easyconfigs/m/Mesa/libGLU-9.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb similarity index 100% rename from easybuild/easyconfigs/m/Mesa/libGLU-9.0.0-intel-2016b.eb rename to easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb -- GitLab From 51c8bbcbda67b2f39554e290644865f9f3b933a3 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 17:52:47 +0200 Subject: [PATCH 327/701] Added deps for Mesa --- .../Mako-1.0.4-intel-2016b-Python-2.7.12.eb | 22 +++++++++++++++ .../n/nettle/nettle-3.2-intel-2016b.eb | 28 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..4817748dbc --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb new file mode 100644 index 0000000000..728d252367 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.2' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' -- GitLab From f4f58a11d064edd60f218ae6a7b80d6516d5acf9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 17:53:14 +0200 Subject: [PATCH 328/701] Updated Mesa deps --- .../m/Mesa/Mesa-12.0.1-intel-2016b.eb | 22 ++++++++----------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb index c6932e7252..c421b33e7c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb @@ -1,3 +1,10 @@ +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + easyblock = 'ConfigureMake' name = 'Mesa' @@ -24,27 +31,18 @@ builddependencies = [ ] dependencies = [ - ('libxml2', '2.9.4'), + ('Mako', '1.0.4'), + ('nettle', '3.2'), ('X11', '20160819'), ('libdrm', '2.4.70'), ('LLVM', '3.8.1'), -# ('eudev', '3.1.5'), ] -# Use the os provided libudev or the EB provided eudev -osdependencies = ['libudev'] - # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " -# package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' -#preconfigopts = ' libtoolize && ' - -#prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" CFLAGS= ' - sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', @@ -53,6 +51,4 @@ sanity_check_paths = { 'dirs': [] } -maxparallel = 1 - moduleclass = 'vis' -- GitLab From 3d3b4d06c5d1f264a1a7d4793524044fc51a133c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 17:58:36 +0200 Subject: [PATCH 329/701] Correct versionsuffix --- easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb index c421b33e7c..014dfb4944 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb @@ -31,7 +31,7 @@ builddependencies = [ ] dependencies = [ - ('Mako', '1.0.4'), + ('Mako', '1.0.4', '-Python-2.7.12'), ('nettle', '3.2'), ('X11', '20160819'), ('libdrm', '2.4.70'), -- GitLab From bb8cd3ad96829090b30765f12e173548ddd970c9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 Aug 2016 18:06:26 +0200 Subject: [PATCH 330/701] Downgrade to build deps --- easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb | 4 +++- easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb | 1 + 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb index 014dfb4944..1b4d5ebc13 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb @@ -28,10 +28,12 @@ builddependencies = [ ('Bison', '3.0.4'), ('Autotools', '20150215'), ('pkg-config', '0.29.1'), + ('Mako', '1.0.4', '-Python-2.7.12'), + ('zlib', '1.2.8'), + ('libxml2', '2.9.4'), ] dependencies = [ - ('Mako', '1.0.4', '-Python-2.7.12'), ('nettle', '3.2'), ('X11', '20160819'), ('libdrm', '2.4.70'), diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb index 9eede49210..ee021a1cfc 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require the X11 to be present. configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' -- GitLab From bdcad38bf4e48f671c4457cc0c6d16172d8fd4c6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 25 Aug 2016 10:03:05 +0200 Subject: [PATCH 331/701] Add python enabled libxml2 for Mesa --- ...libxml2-2.9.4-intel-2016b-Python-2.7.12.eb | 33 +++++++++++++++++++ .../m/Mesa/Mesa-12.0.1-intel-2016b.eb | 6 ++-- 2 files changed, 36 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..8f6fcf8992 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb index 1b4d5ebc13..821ca3a0b7 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb @@ -29,15 +29,15 @@ builddependencies = [ ('Autotools', '20150215'), ('pkg-config', '0.29.1'), ('Mako', '1.0.4', '-Python-2.7.12'), - ('zlib', '1.2.8'), - ('libxml2', '2.9.4'), + ('libxml2', '2.9.4', '-Python-2.7.12'), ] dependencies = [ + ('zlib', '1.2.8'), ('nettle', '3.2'), - ('X11', '20160819'), ('libdrm', '2.4.70'), ('LLVM', '3.8.1'), + ('X11', '20160819'), ] # GLU is not part anymore of Mesa package! -- GitLab From 5f511f644ac6ea66e9dbcdeab7c869d03d235284 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 25 Aug 2016 10:18:55 +0200 Subject: [PATCH 332/701] Use EB python in libxml2 --- .../l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb index 8f6fcf8992..d326810b20 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb @@ -18,7 +18,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB --with-python=$EBROOTPYTHON/bin/python' dependencies = [ ('zlib', '1.2.8'), -- GitLab From fae007ae72e5610f76f31de32d638bbdc3fa8831 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 1 Sep 2016 09:39:28 +0200 Subject: [PATCH 333/701] Don't build Tkinter in Python as it requires X11 Build the Tk module for Python requires a full X11 stack. We want to avoid that. --- easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb index e77dca8172..42a21bb5f7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb @@ -18,7 +18,8 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + # We don't build Tkinter as it requires an X11 stack + # ('Tk', '8.6.5'), ('GMP', '6.1.1'), ('libffi', '3.2.1'), # OS dependency should be preferred if the os version is more recent then this version, -- GitLab From 113996fc6cc675581b4b400f0be815511d62fe6d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 1 Sep 2016 10:16:08 +0200 Subject: [PATCH 334/701] Add Clang/LLVM 3.9 --- .../c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb | 49 +++++++++++++++++++ .../l/LLVM/LLVM-3.9.0-foss-2016b.eb | 42 ++++++++++++++++ .../l/LLVM/LLVM-3.9.0-intel-2016b.eb | 42 ++++++++++++++++ 3 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..277005ae82 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.9.0" + +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': '5.4.0-2.26'} +# 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", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.1'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12', '-bare'), + ('libxml2', '2.9.4'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb new file mode 100644 index 0000000000..15f53abe54 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.9.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb new file mode 100644 index 0000000000..bed6b7ed50 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.9.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From 7d1759c4f74c316b81667b6c858c0ef61d80c709 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 1 Sep 2016 10:23:33 +0200 Subject: [PATCH 335/701] Use libxml2 easyblock for Python --- .../l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb index d326810b20..c0c3697f83 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.4' versionsuffix = '-Python-%(pyver)s' @@ -18,16 +16,11 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB --with-python=$EBROOTPYTHON/bin/python' +configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' dependencies = [ ('zlib', '1.2.8'), ('Python', '2.7.12'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' -- GitLab From f2a94270eba46753dfa0e872ce11a2e54577cf1e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 31 Aug 2016 17:50:22 +0200 Subject: [PATCH 336/701] Add CMake/3.6.1 for intel/2016b --- .../c/CMake/CMake-3.6.1-intel-2016b.eb | 33 +++++++++++++++++++ .../c/CMake/CMake-3.6.1-use-gnu11.patch | 14 ++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb new file mode 100644 index 0000000000..40d915d152 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +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': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s-use-gnu11.patch'] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # 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', '1.0.1s'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch new file mode 100644 index 0000000000..2a6ab800b5 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch @@ -0,0 +1,14 @@ +diff -ur cmake-3.6.1.orig/Modules/Compiler/Intel-C.cmake cmake-3.6.1/Modules/Compiler/Intel-C.cmake +--- cmake-3.6.1.orig/Modules/Compiler/Intel-C.cmake 2016-07-22 15:50:22.000000000 +0200 ++++ cmake-3.6.1/Modules/Compiler/Intel-C.cmake 2016-08-31 17:32:38.594401777 +0200 +@@ -15,8 +15,8 @@ + endif() + + if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 15.0.0) +- set(CMAKE_C11_STANDARD_COMPILE_OPTION "${_std}=c11") +- set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=c11") ++ set(CMAKE_C11_STANDARD_COMPILE_OPTION "${_std}=gnu11") ++ set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=gnu11") + endif() + + if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 12.1) -- GitLab From 91e69a009959e4a51235d9143434f73363682c20 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 1 Sep 2016 11:01:56 +0200 Subject: [PATCH 337/701] Add comment in patch about it's purpose --- easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch index 2a6ab800b5..361f38b0b3 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch @@ -1,14 +1,17 @@ +# Using -std=c11 lets the build fail with very weird errors (with icc). Switching to +# gnu11 makes it pass. +# Ward Poelmans diff -ur cmake-3.6.1.orig/Modules/Compiler/Intel-C.cmake cmake-3.6.1/Modules/Compiler/Intel-C.cmake --- cmake-3.6.1.orig/Modules/Compiler/Intel-C.cmake 2016-07-22 15:50:22.000000000 +0200 +++ cmake-3.6.1/Modules/Compiler/Intel-C.cmake 2016-08-31 17:32:38.594401777 +0200 @@ -15,8 +15,8 @@ endif() - + if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 15.0.0) - set(CMAKE_C11_STANDARD_COMPILE_OPTION "${_std}=c11") - set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=c11") + set(CMAKE_C11_STANDARD_COMPILE_OPTION "${_std}=gnu11") + set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=gnu11") endif() - + if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 12.1) -- GitLab From db856d24fb844913f7553b3d169259010d8d1fe2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 1 Sep 2016 11:43:51 +0200 Subject: [PATCH 338/701] Add patch for LLVM + intel compiler --- .../l/LLVM/LLVM-3.9.0-intel-2016b.eb | 2 ++ .../l/LLVM/LLVM-3.9.0-intel-fix-loop.patch | 26 +++++++++++++++++++ 2 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-fix-loop.patch diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb index bed6b7ed50..23f87e242d 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb @@ -18,6 +18,8 @@ toolchainopts = {'cstd': 'gnu++11'} source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] +patches = ['LLVM-3.9.0-intel-fix-loop.patch'] + builddependencies = [ ('CMake', '3.6.1'), ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-fix-loop.patch b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-fix-loop.patch new file mode 100644 index 0000000000..33e6578be4 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-fix-loop.patch @@ -0,0 +1,26 @@ +# Bug in intel compiler +# Source: From https://sft.its.cern.ch/jira/browse/ROOT-8233 +diff -ur llvm-3.9.0rc3.src.orig/lib/Transforms/Utils/LoopUtils.cpp llvm-3.9.0rc3.src/lib/Transforms/Utils/LoopUtils.cpp +--- llvm-3.9.0rc3.src.orig/lib/Transforms/Utils/LoopUtils.cpp 2016-06-11 23:48:25.000000000 +0200 ++++ llvm-3.9.0rc3.src/lib/Transforms/Utils/LoopUtils.cpp 2016-09-01 11:40:34.394205219 +0200 +@@ -834,6 +834,11 @@ + return UsedOutside; + } + ++namespace llvm { ++ extern char &LoopSimplifyID; ++ extern char &LCSSAID; ++} ++ + void llvm::getLoopAnalysisUsage(AnalysisUsage &AU) { + // By definition, all loop passes need the LoopInfo analysis and the + // Dominator tree it depends on. Because they all participate in the loop +@@ -845,8 +850,6 @@ + + // We must also preserve LoopSimplify and LCSSA. We locally access their IDs + // here because users shouldn't directly get them from this header. +- extern char &LoopSimplifyID; +- extern char &LCSSAID; + AU.addRequiredID(LoopSimplifyID); + AU.addPreservedID(LoopSimplifyID); + AU.addRequiredID(LCSSAID); -- GitLab From 0fcdbad50b143fddf9bd3735d91b87eea34fbc22 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 1 Sep 2016 12:03:49 +0200 Subject: [PATCH 339/701] Do release build for LLVM --- easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb | 3 ++- easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb index 15f53abe54..2a5106af44 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb @@ -30,7 +30,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' # required to install extra tools in bin/ -configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb index 23f87e242d..2bf426d402 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb @@ -32,7 +32,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' # required to install extra tools in bin/ -configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], -- GitLab From a0485b6337c89e1b1b2236d66a5d2c7312835000 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 1 Sep 2016 13:21:12 +0200 Subject: [PATCH 340/701] Cppcheck easyconfig --- .../c/cppcheck/cppcheck-1.75-intel-2015b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb diff --git a/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb b/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb new file mode 100644 index 0000000000..8c689004f0 --- /dev/null +++ b/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb @@ -0,0 +1,20 @@ +name = 'cppcheck' +version = '1.75' + +homepage = 'http://cppcheck.sourceforge.net/' +description = """Cppcheck is a static analysis tool for C/C++ code""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.bz2'] + +dependencies = [ + ('Qt5', '5.5.1'), + ('PCRE', '8.37'), +] + +have_rules = True +build_gui = True + +moduleclass = 'lang' -- GitLab From 172b71ea013a9d02e6783bf63199d097bd7f380a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Sep 2016 13:32:08 +0200 Subject: [PATCH 341/701] clean up libxml2 easyconfigs according to updated libxml2 easyblock --- ...bxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 14 ++------------ .../l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb | 9 --------- .../libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb | 14 ++------------ .../l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb | 9 --------- .../libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb | 14 ++------------ .../l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb | 9 --------- .../libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb | 14 ++------------ .../libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb | 14 ++------------ .../l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb | 9 --------- .../libxml2-2.8.0-intel-2015a-Python-2.7.3.eb | 14 ++------------ .../l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb | 9 --------- .../l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb | 10 +--------- .../l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb | 9 --------- .../l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb | 9 --------- .../l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb | 9 --------- .../l/libxml2/libxml2-2.9.1-foss-2015b.eb | 10 ---------- .../l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb | 9 --------- .../l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb | 9 --------- .../libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb | 9 --------- .../libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb | 9 --------- .../libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb | 3 +-- .../l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb | 9 --------- .../l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb | 9 --------- .../l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb | 9 --------- .../l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb | 9 --------- .../l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb | 9 --------- .../l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb | 9 --------- .../libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb | 14 ++------------ .../l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb | 9 --------- .../l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb | 9 --------- .../l/libxml2/libxml2-2.9.1-intel-2014b.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb | 10 +--------- .../l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-foss-2015a.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-foss-2015b.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-intel-2014.06.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-intel-2014b.eb | 9 --------- .../libxml2-2.9.2-intel-2015a-Python-2.7.10.eb | 9 ++------- .../libxml2-2.9.2-intel-2015a-Python-2.7.9.eb | 9 ++------- .../l/libxml2/libxml2-2.9.2-intel-2015a.eb | 9 --------- .../l/libxml2/libxml2-2.9.2-intel-2015b.eb | 9 --------- .../l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb | 11 ----------- .../l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb | 11 ----------- .../libxml2-2.9.3-foss-2015a-Python-2.7.11.eb | 9 ++------- .../l/libxml2/libxml2-2.9.3-foss-2015a.eb | 6 ------ .../libxml2-2.9.3-foss-2016a-Python-2.7.11.eb | 2 -- .../l/libxml2/libxml2-2.9.3-foss-2016a.eb | 11 ----------- .../l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb | 11 ----------- .../l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb | 11 ----------- .../libxml2-2.9.3-intel-2015b-Python-2.7.10.eb | 9 ++------- .../libxml2-2.9.3-intel-2015b-Python-2.7.11.eb | 9 ++------- .../libxml2-2.9.3-intel-2016a-Python-2.7.11.eb | 9 ++------- .../l/libxml2/libxml2-2.9.3-intel-2016a.eb | 11 ----------- .../l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb | 9 --------- .../l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb | 11 ----------- .../l/libxml2/libxml2-2.9.4-foss-2016a.eb | 11 ----------- .../l/libxml2/libxml2-2.9.4-foss-2016b.eb | 11 ----------- .../l/libxml2/libxml2-2.9.4-intel-2016b.eb | 11 ----------- 63 files changed, 29 insertions(+), 580 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 e98bac6018..61ac8b0f98 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 @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 4a4a4816ab..b5be030eb8 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.8.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb index e1868be130..b18cebf5ed 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -13,20 +14,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 00021cddc9..8dce8ccf02 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.8.0' @@ -15,13 +13,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb index b82e8e6c93..541f5b23a7 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 91e1ffbc9c..e30ea6f810 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.8.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb index 31e824b5ea..a089a50337 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 5a92ef8bcb..ecc03cc898 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 @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb index 98b15d6f97..e6c885e909 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.8.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 3f185c7e6d..b3162eb734 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 @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb index 0567c075f0..d27cd00a3d 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 ee43d716e2..437c090f56 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 @@ -1,11 +1,10 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' 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': '1.4.10'} toolchainopts = {'pic': True} @@ -15,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb index 06cdc26c76..7012fe4e03 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 3042a3cf37..c071752aa8 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb index f0aa6dee9c..de12c4768f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb index 03c075bd1a..4a999c8acc 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -17,13 +15,5 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] - -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb index 33b6562e0f..dacb6f49da 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 e44ddd0d64..db9d8e9f00 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb index 90b9bc8ea5..fe5357a0ea 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 487bf333ac..3549a11503 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb index ae7f22f7a4..758bb9dd84 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -7,6 +7,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -14,8 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - dependencies = [ ('zlib', '1.2.8'), ('Python', '2.7.5'), 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 5448805458..4e5a1b7c92 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb index b09000568f..ef65dcb9ac 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 3e1cc77790..49bef39036 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb index 5da6298832..bbaaf19893 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 aa7e4b1f77..c4fbddee11 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb index e50f08d5e3..345f7339bb 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 9d4e84392a..0cdd2e03c2 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 @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.6' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.6'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb index 0cdacffa3a..35cce5f832 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 ca67a911c1..9322eb079f 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb index c6335dd8b2..7322bbf1cf 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - 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 index 173e4c1870..47732da727 100644 --- 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -9,6 +7,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'GCC', 'version': '4.8.3'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -16,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb index 841eddc11e..84f6203208 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb index 8d892b499f..80b60e88be 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb index 3c33fb41da..8fb7cc97f0 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 ae39cc8c24..0d7eb11ba2 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb index ad02e51c2e..933fed03d3 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 f232e382c0..935739296d 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb index 54c5dad803..22db63d4d8 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' 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 index 22d8c149d6..42669ee57d 100644 --- 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb index acdd85b6e6..947a255ee9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - '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 22aefe7d0c..d0e28b4178 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 @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb index 37724f23f1..b4846f1d26 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.10' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.10'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb index 307b1793d4..af7eb40b20 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.9'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb index 1a4f4c99c4..28e034ab2c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb index b95f92dfd9..a9be901465 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb index 322d4dbeda..135641e29d 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb @@ -1,6 +1,4 @@ # contributed by Luca Marsella (CSCS) -easyblock = 'ConfigureMake' - name = 'libxml2' version = "2.9.3" @@ -18,15 +16,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb index 9e15ece882..4447186030 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -16,15 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb index 6cafc86e4f..38a9a0dfbc 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.11' -pythonshortver = '.'.join(pythonver.split('.')[:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.11'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb index ad525d1e63..3f244ca271 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -16,12 +14,8 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [ ('zlib', '1.2.8'), ] -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb index 0df5cbd957..5c76876c0d 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -15,8 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - dependencies = [ ('zlib', '1.2.8'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb index ed32688bef..45737f40c5 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -17,15 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb index cd5c7d2c15..b5f12f37c2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -17,15 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb index d7a623361a..116952d9c8 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -17,15 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb index 34777c9cc6..f919243b0f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.10' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.10'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb index b28071061a..95fbcbd2d4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.11' -pythonshortver = '.'.join(pythonver.split('.')[:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.11'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb index 41e2af0e98..b50b2e930b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-Python-%s' % pyver - dependencies = [ ('zlib', '1.2.8'), - ('Python', pyver), + ('Python', '2.7.11'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb index d29bab77ba..483a54f92a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -17,15 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb index 980c2fea95..6000926382 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.4' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb index 96e7f21c7d..6e41adde06 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.4' @@ -17,8 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - builddependencies = [ ('binutils', '2.25'), ] @@ -27,11 +23,4 @@ dependencies = [ ('zlib', '1.2.8'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb index b6ee64dbb7..e6cae21695 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.4' @@ -17,15 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb index d1806d2536..09ede640fb 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.4' @@ -17,15 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb index 01feb5f8e8..b41d38c545 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.4' @@ -17,15 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - -modextrapaths = {'CPATH': ['include/libxml2']} - moduleclass = 'lib' -- GitLab From aeb216933fde05b044a78619b3189f6bee3255c8 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 1 Sep 2016 13:57:41 +0200 Subject: [PATCH 342/701] Update to Libint/2.1.0 and intel/2016b --- ...Python-2.7.11.eb => Libint-2.1.0-intel-2016b-Python-2.7.12.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/Libint/{Libint-2.0.5-intel-2016a-Python-2.7.11.eb => Libint-2.1.0-intel-2016b-Python-2.7.12.eb} (100%) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb similarity index 100% rename from easybuild/easyconfigs/l/Libint/Libint-2.0.5-intel-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb -- GitLab From f8fd9d6253a8a2d3d7135833691e2bb11daf6f63 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 1 Sep 2016 14:04:27 +0200 Subject: [PATCH 343/701] Update to version 2.1.0 and intel/2016b --- .../l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb index c56a331e40..a3a27a4207 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb @@ -1,21 +1,21 @@ name = 'Libint' -version = '2.0.5' +version = '2.1.0' # Some stuff that uses Libint (PSI) needs Boost-Python, so we inherit the versionsuffix here: #1421 -versionsuffix = '-Python-2.7.11' +versionsuffix = '-Python-2.7.12' homepage = 'https://github.com/evaleev/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': 'intel', 'version': '2016a'} +toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/evaleev/libint/archive/'] dependencies = [ - ('GMP', '6.1.0'), - ('Boost', '1.60.0', versionsuffix), + ('GMP', '6.1.1'), + ('Boost', '1.61.0', versionsuffix), ] builddependencies = [('Autotools', '20150215')] -- GitLab From 19158539869216ac5bbc07f26c31c285f10e00e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Sep 2016 15:23:26 +0200 Subject: [PATCH 344/701] add easyconfig DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb, add easyconfig MariaDB-10.1.17-intel-2016b.eb, add easyconfig jemalloc-4.2.1-intel-2016b.eb --- ...DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb | 36 ++++++++++++++++ .../j/jemalloc/jemalloc-4.2.1-intel-2016b.eb | 28 +++++++++++++ .../m/MariaDB/MariaDB-10.1.17-intel-2016b.eb | 42 +++++++++++++++++++ 3 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..0a65c07d0f --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.033' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~capttofu/DBD-mysql-%(version)s/' +description = """Perl binding for MySQL""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/C/CA/CAPTTOFU/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.24.0'), + ('MariaDB', '10.1.17'), + ('zlib', '1.2.8'), + # 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', '1.0.1q'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# force static linking of libmysqlclient to dance around problem with unresolved symbols +configopts = '--libs="-L$EBROOTMARIADB/lib -Wl,-Bstatic -lmysqlclient -Wl,-Bdynamic -lpthread -lz -lrt -lssl -lcrypto"' + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.1-intel-2016b.eb new file mode 100644 index 0000000000..7ab95453f8 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.1-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.2.1' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " +prebuildopts = "make dist && " + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb new file mode 100644 index 0000000000..25dc98c07b --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.1.17' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'MariaDB-10.1.13-remove-Werror.patch', + 'MariaDB-10.1.13-link-rt-for-jemalloc.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('ncurses', '6.0'), + ('jemalloc', '4.2.1'), + ('PCRE', '8.39'), + ('XZ', '5.2.2'), + ('Boost', '1.61.0', '-Python-2.7.12'), + ('libxml2', '2.9.4'), +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'data' -- GitLab From 603292170c6bb2ab1bbdfb94f1de7e78efd331cb Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 1 Sep 2016 16:15:52 +0200 Subject: [PATCH 345/701] Fixing the cppcheck easyconfig --- easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb b/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb index 8c689004f0..70ed0f8ae7 100644 --- a/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb +++ b/easybuild/easyconfigs/c/cppcheck/cppcheck-1.75-intel-2015b.eb @@ -5,6 +5,7 @@ homepage = 'http://cppcheck.sourceforge.net/' description = """Cppcheck is a static analysis tool for C/C++ code""" toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-%(version)s.tar.bz2'] @@ -17,4 +18,6 @@ dependencies = [ have_rules = True build_gui = True +buildopts = 'CXXFLAGS="$CXXFLAGS -std=c++11"' + moduleclass = 'lang' -- GitLab From 7e1204762f7c2befcfc9c7e731f3a04126dd9130 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Thu, 1 Sep 2016 16:35:54 +0200 Subject: [PATCH 346/701] Version of MIRA using the foss 2016a toolchain including an updated version of the dependency gperftools. --- .../g/gperftools/gperftools-2.5-foss-2016a.eb | 24 +++++++++++++ .../MIRA-4.0.2-foss-2016a-Python-2.7.11.eb | 36 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb create mode 100644 easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb new file mode 100644 index 0000000000..6dd4849514 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = "gperftools" +version = "2.5" + +homepage = 'http://github.com/gperftools/gperftools' +description = """gperftools are for use by developers so that they can create more robust applications. + Especially of use to those developing multi-threaded applications in C++ with templates. + Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] + +builddependencies = [('Autotools', '20150215', '', ('GCCcore', '4.9.3'))] +dependencies = [('libunwind', '1.1')] + +sanity_check_paths = { + 'files': ["bin/pprof"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..c98b95b63b --- /dev/null +++ b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'MIRA' +version = '4.0.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://sourceforge.net/p/mira-assembler/wiki/Home/' +description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), + IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s.tar.bz2'] +source_urls = [('http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/', 'download')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = '--with-boost-libdir=$EBROOTBOOST/lib --with-expat=$EBROOTEXPAT' + +patches = ['MIRA-%(version)s-quirks.patch'] + +builddependencies = [('flex', '2.5.39')] +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('expat', '2.1.1'), + ('zlib', '1.2.8'), + ('gperftools', '2.5'), +] + +sanity_check_paths = { + 'files': ["bin/mira"], + 'dirs': ["bin", "share"], +} + +moduleclass = 'bio' -- GitLab From ff02a1d1351ede7c16699e701c8c8cbce68d4cf5 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Thu, 1 Sep 2016 16:02:42 +0100 Subject: [PATCH 347/701] Circos 0.69-2 using ictce 5.5.0 toolchain --- .../Circos-0.69-2-ictce-5.5.0-Perl-5.18.2.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/Circos/Circos-0.69-2-ictce-5.5.0-Perl-5.18.2.eb diff --git a/easybuild/easyconfigs/c/Circos/Circos-0.69-2-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/c/Circos/Circos-0.69-2-ictce-5.5.0-Perl-5.18.2.eb new file mode 100644 index 0000000000..6c93e5f90f --- /dev/null +++ b/easybuild/easyconfigs/c/Circos/Circos-0.69-2-ictce-5.5.0-Perl-5.18.2.eb @@ -0,0 +1,33 @@ +easyblock = "Tarball" + +name = 'Circos' +version = '0.69-2' + +homepage = 'http://www.circos.ca/' +description = """Circos is a software package for visualizing data and information. + It visualizes data in a circular layout - this makes Circos ideal for exploring + relationships between objects or positions.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://circos.ca/distribution/'] +sources = [SOURCELOWER_TGZ] + +perl = 'Perl' +perlver = '5.18.2' +versionsuffix = '-%s-%s' % (perl, perlver) +dependencies = [ + (perl, perlver), + ('GD', '2.52', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/%(name)s'], +} + +modextrapaths = {'PERL5LIB': 'lib'} + +sanity_check_commands = [('perl', '-e "use Circos"')] + +moduleclass = 'bio' -- GitLab From 20e2f6940ade9b8d19e387650804cbfebdb6d592 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 1 Sep 2016 17:26:33 +0200 Subject: [PATCH 348/701] Drop Clang/3.9.0 for now Build issues, will try to fix them later in another PR. --- .../c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb | 49 ------------------- 1 file changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb deleted file mode 100644 index 277005ae82..0000000000 --- a/easybuild/easyconfigs/c/Clang/Clang-3.9.0-GCC-5.4.0-2.26.eb +++ /dev/null @@ -1,49 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans -# Authors:: Dmitri Gribenko -# Authors:: Ward Poelmans -# License:: GPLv2 or later, MIT, three-clause BSD. -# $Id$ -## - -name = "Clang" -version = "3.9.0" - -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': '5.4.0-2.26'} -# 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", - "openmp-%(version)s.src.tar.xz", -] - -dependencies = [ - ('GMP', '6.1.1'), -] - -builddependencies = [ - ('CMake', '3.6.1'), - ('Python', '2.7.12', '-bare'), - ('libxml2', '2.9.4'), -] - -assertions = True - -usepolly = True - -build_targets = ['X86'] - -moduleclass = 'compiler' -- GitLab From 6871ffa1a51ebf15b941f4ed077fb4b53b9b21a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Sep 2016 19:31:19 +0200 Subject: [PATCH 349/701] add easyconfig MariaDB-10.1.17-intel-2016b.eb --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb index 25dc98c07b..fe8145c64d 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.17-intel-2016b.eb @@ -32,6 +32,7 @@ separate_build_dir = True configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON " configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITHOUT_TOKUDB=ON " # not supported with Intel compilers sanity_check_paths = { 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, -- GitLab From 6b8e69325f19fe78df7f071514fbb266e163f487 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 2 Sep 2016 11:17:07 +0200 Subject: [PATCH 350/701] Update libint/2.1.0 to work --- .../Libint-2.1.0-intel-2016b-Python-2.7.12.eb | 28 ---------------- .../l/Libint/Libint-2.1.0-intel-2016b.eb | 33 +++++++++++++++++++ 2 files changed, 33 insertions(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb deleted file mode 100644 index a3a27a4207..0000000000 --- a/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'Libint' -version = '2.1.0' -# Some stuff that uses Libint (PSI) needs Boost-Python, so we inherit the versionsuffix here: #1421 -versionsuffix = '-Python-2.7.12' - -homepage = 'https://github.com/evaleev/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': 'intel', 'version': '2016b'} -toolchainopts = {'pic': True} - -sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] -source_urls = ['https://github.com/evaleev/libint/archive/'] - -dependencies = [ - ('GMP', '6.1.1'), - ('Boost', '1.61.0', versionsuffix), -] - -builddependencies = [('Autotools', '20150215')] - -# no exec perm on the autogen.sh script -preconfigopts = 'sh autogen.sh && ' - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb new file mode 100644 index 0000000000..6b33080439 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Libint' +version = '2.1.0' + +homepage = 'https://github.com/evaleev/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': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['libint-%(version)s-stable.tgz'] +source_urls = ['https://github.com/evaleev/libint/releases/download/v%(version)s'] + +builddependencies = [ + ('GMP', '6.1.1'), + ('Boost', '1.61.0', '-Python-2.7.12'), + ('Eigen', '3.2.9'), + ('Python', '2.7.12'), +] + +configopts = '--enable-shared' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/libint2.h', 'include/libint2.hpp', + 'lib/libint2.a', 'lib/libint2.%s' % SHLIB_EXT], + 'dirs': ['share/libint', 'include/libint2', 'lib/pkgconfig'] +} + +moduleclass = 'chem' -- GitLab From b34f9a9f5af18ae285904c9d1e82de7ae87a5074 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 2 Sep 2016 12:26:59 +0200 Subject: [PATCH 351/701] add easyconfig gperftools-2.5-intel-2016b.eb, add easyconfig libunwind-1.1-intel-2016b.eb --- .../gperftools/gperftools-2.5-intel-2016b.eb | 26 +++++++++++++++ .../l/libunwind/libunwind-1.1-intel-2016b.eb | 33 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb new file mode 100644 index 0000000000..2144d90378 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = "gperftools" +version = "2.5" + +homepage = 'http://github.com/gperftools/gperftools' +description = """gperftools are for use by developers so that they can create more robust applications. + Especially of use to those developing multi-threaded applications in C++ with templates. + Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] + +builddependencies = [('Autotools', '20150215')] +dependencies = [('libunwind', '1.1')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ["bin/pprof"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb new file mode 100644 index 0000000000..aea3c64e51 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' -- GitLab From 95f5414f1f90e278ef84eb1e5409831637dc4a5c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 2 Sep 2016 12:30:40 +0200 Subject: [PATCH 352/701] add easyconfig gperftools-2.5-intel-2016b.eb --- .../easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb index 2144d90378..fbae9a2a85 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-intel-2016b.eb @@ -13,10 +13,9 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] -builddependencies = [('Autotools', '20150215')] dependencies = [('libunwind', '1.1')] -preconfigopts = './autogen.sh && ' +configopts = '--enable-libunwind' sanity_check_paths = { 'files': ["bin/pprof"], -- GitLab From 4af1dacbc72aa931d38b57f34e358b295031d790 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 2 Sep 2016 12:46:09 +0200 Subject: [PATCH 353/701] use updated Libint easyblock --- .../easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb index 6b33080439..8282cb93cc 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.1.0-intel-2016b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'Libint' version = '2.1.0' @@ -20,14 +18,4 @@ builddependencies = [ ('Python', '2.7.12'), ] -configopts = '--enable-shared' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['include/libint2.h', 'include/libint2.hpp', - 'lib/libint2.a', 'lib/libint2.%s' % SHLIB_EXT], - 'dirs': ['share/libint', 'include/libint2', 'lib/pkgconfig'] -} - moduleclass = 'chem' -- GitLab From c9b4ca890e48d0023f2f86df2998672753323a28 Mon Sep 17 00:00:00 2001 From: jhein32 Date: Fri, 2 Sep 2016 12:59:05 +0200 Subject: [PATCH 354/701] First complete fileset for an pomkl, using openmpi 1.10.4 and mkl 11.3.3.210 --- .../h/HPL/HPL-2.1-pomkl-2016.09.eb | 18 ++++++++ .../h/HPL/HPL-2.2-pomkl-2016.09.eb | 18 ++++++++ .../hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb | 27 ++++++++++++ .../i/imkl/imkl-11.3.3.210-pompi-2016.09.eb | 38 +++++++++++++++++ .../OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb | 41 +++++++++++++++++++ .../easyconfigs/p/pomkl/pomkl-2016.09.eb | 20 +++++++++ .../easyconfigs/p/pompi/pompi-2016.09.eb | 19 +++++++++ 7 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb create mode 100644 easybuild/easyconfigs/p/pompi/pompi-2016.09.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb new file mode 100644 index 0000000000..112d6aa634 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.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': 'pomkl', 'version': '2016.09'} +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-2.2-pomkl-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb new file mode 100644 index 0000000000..005a57564c --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +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': 'pomkl', 'version': '2016.09'} +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-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..6138766fd9 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.4' + +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': 'PGI', 'version': '16.7-GCC-5.4.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['b6f23eb59074fd09fdd84905d50b103d'] + +dependencies = [ + ('numactl', '2.0.11', '', ('GCCcore', '5.4.0')), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb new file mode 100644 index 0000000000..ea94f4aa6a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '11.3.3.210' + +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': 'pompi', 'version': '2016.09'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +components = ['intel-mkl'] + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..fd6bb36c38 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.4' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'PGI', 'version': '16.7-GCC-5.4.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +checksums = ['fb2fdb6a5b65c80d7dfa4bc9a0caf665'] + +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 +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify + +dependencies = [('hwloc', '1.11.4')] + +# 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 libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +sanity_check_commands = [ + ('mpicc --version | grep pgcc', ''), + ('mpicxx --version | grep pgc++', ''), + ('mpifort --version | grep pgfortran', ''), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb new file mode 100644 index 0000000000..74076e42f0 --- /dev/null +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'pomkl' +version = '2016.09' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.7' +gccsuff = '-GCC-5.4.0-2.26' + +dependencies = [ + ('PGI', compver, gccsuff), + ('OpenMPI', '1.10.4', '', ('PGI', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('pompi', '%s' % (version))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb new file mode 100644 index 0000000000..b83ba47007 --- /dev/null +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'pompi' +version = '2016.09' +pgisuffix = '-GCC-5.4.0-2.26' + +homepage = 'http://www.pgroup.com/index.htm' +description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '16.7' + +dependencies = [ + ('PGI', compver, pgisuffix), + ('OpenMPI', '1.10.4', '', ('PGI', '%s%s' % (compver, pgisuffix))), +] + +moduleclass = 'toolchain' -- GitLab From f86546c585c9d6c0c862faaf6676b85d7cd47f90 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Fri, 2 Sep 2016 14:15:37 +0100 Subject: [PATCH 355/701] foss 2016.07 toolchain (uses GCC 6.1.0) --- .../b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb | 26 + .../b/binutils/binutils-2.27-GCCcore-6.1.0.eb | 21 + .../f/FFTW/FFTW-3.3.4-gompi-2016.07.eb | 34 ++ .../f/flex/flex-2.6.0-GCCcore-6.1.0.eb | 21 + easybuild/easyconfigs/f/foss/foss-2016.07.eb | 37 ++ easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb | 25 + .../easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 57 +++ .../GCCcore/GCCcore-6.1.0_fix-find-isl.patch | 14 + ...6.1.0_mpfr-3.1.4-allpatches-20160804.patch | 455 ++++++++++++++++++ .../easyconfigs/g/gompi/gompi-2016.07.eb | 22 + .../h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb | 23 + .../m/M4/M4-1.4.17-GCCcore-6.1.0.eb | 26 + ...nBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb | 49 ++ .../OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb | 33 ++ ...pi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb | 25 + .../z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb | 25 + 16 files changed, 893 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.07.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2016.07.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_fix-find-isl.patch create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_mpfr-3.1.4-allpatches-20160804.patch create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2016.07.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..59b38bba21 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +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': 'GCCcore', 'version': '6.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..215aaf0cb2 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.27' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.1.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, 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) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.07.eb new file mode 100644 index 0000000000..3fd16df92f --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.07.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': '2016.07'} +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/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..687cf19d5f --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -0,0 +1,21 @@ +name = 'flex' +version = '2.6.0' + +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': 'GCCcore', 'version': '6.1.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Bison', '3.0.4')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +parallel = 1 + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.07.eb b/easybuild/easyconfigs/f/foss/foss-2016.07.eb new file mode 100644 index 0000000000..f4211bb9f3 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.07.eb @@ -0,0 +1,37 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.07' + +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 = '6.1.0' +binutilsver = '2.27' +gccbinver = '%s-%s' % (gccver, binutilsver) + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.1' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# 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', gccbinver), + ('OpenMPI', '1.10.2', '', ('GCC', gccbinver)), + (blaslib, blasver, blassuff, comp_mpi_tc), + ('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/GCC/GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb new file mode 100644 index 0000000000..258248286e --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '6.1.0' + +binutilsver = '2.27' +versionsuffix = '-%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': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb new file mode 100644 index 0000000000..d15501829b --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -0,0 +1,57 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '6.1.0' + +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': ''} + +mpfr_version = '3.1.4' + +source_urls = [ + '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 + 'http://ftp.heanet.ie/mirrors/gnu/%(namelower)s/%(namelower)s-%(version)s/', # Alternative for GCC + 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.1.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.27'), +] + +patches = [ + ('%s-%s_mpfr-%s-allpatches-20160804.patch' % (name, version, mpfr_version), '../mpfr-%s' % mpfr_version), + ('%s-%s_fix-find-isl.patch' % (name, version)), +] + +checksums = [ + '8fb6cb98b8459f5863328380fbf06bd1', # gcc-6.1.0.tar.bz2 + '4c175f86e11eb32d8bf9872ca3a8e11d', # gmp-6.1.1.tar.bz2 + 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 +] + +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/GCCcore/GCCcore-6.1.0_fix-find-isl.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_fix-find-isl.patch new file mode 100644 index 0000000000..6334b6be35 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_fix-find-isl.patch @@ -0,0 +1,14 @@ +# Don't use libmpc and libmpfr to find libisl +# by wpoely86@gmail.com +diff -ur gcc-6.1.0.orig/configure gcc-6.1.0/configure +--- gcc-6.1.0.orig/configure 2016-08-26 17:51:48.470524515 +0200 ++++ gcc-6.1.0/configure 2016-03-17 23:54:19.000000000 +0100 +@@ -6018,7 +6018,7 @@ + _isl_saved_LIBS=$LIBS + + CFLAGS="${_isl_saved_CFLAGS} ${islinc} ${gmpinc}" +- LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs} ${gmplibs}" ++ LDFLAGS="${_isl_saved_LDFLAGS} ${isllibs}" + LIBS="${_isl_saved_LIBS} -lisl -lgmp" + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for isl 0.16, 0.15, or deprecated 0.14" >&5 diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_mpfr-3.1.4-allpatches-20160804.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_mpfr-3.1.4-allpatches-20160804.patch new file mode 100644 index 0000000000..41748b0345 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_mpfr-3.1.4-allpatches-20160804.patch @@ -0,0 +1,455 @@ +# All mpfr patches as of 2016-08-04, from same pull request for GCC 6.2.0 +# taken from their website: http://www.mpfr.org/mpfr-current/#download +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-04-13 21:22:23.720604013 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-04-13 21:22:23.744603677 +0000 +@@ -0,0 +1 @@ ++unix-check +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-04-13 21:22:23.744603677 +0000 +@@ -1 +1 @@ +-3.1.4 ++3.1.4-p1 +diff -Naurd mpfr-3.1.4-a/src/mpfr-impl.h mpfr-3.1.4-b/src/mpfr-impl.h +--- mpfr-3.1.4-a/src/mpfr-impl.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr-impl.h 2016-04-13 21:22:23.736603789 +0000 +@@ -252,19 +252,6 @@ + # define MPFR_WIN_THREAD_SAFE_DLL 1 + #endif + +-/* Detect some possible inconsistencies under Unix. */ +-#if defined(__unix__) +-# if defined(_WIN32) +-# error "Both __unix__ and _WIN32 are defined" +-# endif +-# if __GMP_LIBGMP_DLL +-# error "__unix__ is defined and __GMP_LIBGMP_DLL is true" +-# endif +-# if defined(MPFR_WIN_THREAD_SAFE_DLL) +-# error "Both __unix__ and MPFR_WIN_THREAD_SAFE_DLL are defined" +-# endif +-#endif +- + #if defined(__MPFR_WITHIN_MPFR) || !defined(MPFR_WIN_THREAD_SAFE_DLL) + extern MPFR_THREAD_ATTR unsigned int __gmpfr_flags; + extern MPFR_THREAD_ATTR mpfr_exp_t __gmpfr_emin; +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4" ++#define MPFR_VERSION_STRING "3.1.4-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-04-13 21:22:23.744603677 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4"; ++ return "3.1.4-p1"; + } +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-05-22 19:59:43.838399677 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-05-22 19:59:43.866399168 +0000 +@@ -0,0 +1 @@ ++add-sub-ui-flags +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-05-22 19:59:43.866399168 +0000 +@@ -1 +1 @@ +-3.1.4-p1 ++3.1.4-p2 +diff -Naurd mpfr-3.1.4-a/src/add_ui.c mpfr-3.1.4-b/src/add_ui.c +--- mpfr-3.1.4-a/src/add_ui.c 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/add_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -49,6 +49,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_add(y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range(y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p1" ++#define MPFR_VERSION_STRING "3.1.4-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub_ui.c mpfr-3.1.4-b/src/sub_ui.c +--- mpfr-3.1.4-a/src/sub_ui.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -52,6 +52,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_sub (y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range (y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-05-22 19:59:43.866399168 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p1"; ++ return "3.1.4-p2"; + } +diff -Naurd mpfr-3.1.4-a/tests/tadd_ui.c mpfr-3.1.4-b/tests/tadd_ui.c +--- mpfr-3.1.4-a/tests/tadd_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tadd_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -69,7 +69,9 @@ + + /* nan + 2394875 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_add_ui (y, x, 2394875L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf + 2394875 == +inf */ +diff -Naurd mpfr-3.1.4-a/tests/tsub_ui.c mpfr-3.1.4-b/tests/tsub_ui.c +--- mpfr-3.1.4-a/tests/tsub_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -96,7 +96,9 @@ + + /* nan - 1 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_sub_ui (y, x, 1L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf - 1 == +inf */ +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-06-01 13:00:30.748711490 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-06-01 13:00:30.772711162 +0000 +@@ -0,0 +1 @@ ++sub1-overflow +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-06-01 13:00:30.772711162 +0000 +@@ -1 +1 @@ +-3.1.4-p2 ++3.1.4-p3 +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p2" ++#define MPFR_VERSION_STRING "3.1.4-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub1.c mpfr-3.1.4-b/src/sub1.c +--- mpfr-3.1.4-a/src/sub1.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub1.c 2016-06-01 13:00:30.760711326 +0000 +@@ -96,16 +96,15 @@ + /* A = S*ABS(B) +/- ulp(a) */ + MPFR_SET_EXP (a, MPFR_GET_EXP (b)); + MPFR_RNDRAW_EVEN (inexact, a, MPFR_MANT (b), MPFR_PREC (b), +- rnd_mode, MPFR_SIGN (a), +- if (MPFR_UNLIKELY ( ++MPFR_EXP (a) > __gmpfr_emax)) +- inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a))); +- /* inexact = mpfr_set4 (a, b, rnd_mode, MPFR_SIGN (a)); */ ++ rnd_mode, MPFR_SIGN (a), ++ MPFR_EXP (a)); + if (inexact == 0) + { + /* a = b (Exact) + But we know it isn't (Since we have to remove `c') + So if we round to Zero, we have to remove one ulp. + Otherwise the result is correctly rounded. */ ++ /* An overflow is not possible. */ ++ MPFR_ASSERTD (MPFR_EXP (a) <= __gmpfr_emax); + if (MPFR_IS_LIKE_RNDZ (rnd_mode, MPFR_IS_NEG (a))) + { + mpfr_nexttozero (a); +@@ -136,9 +135,14 @@ + i.e. inexact= MPFR_EVEN_INEX */ + if (MPFR_UNLIKELY (inexact == MPFR_EVEN_INEX*MPFR_INT_SIGN (a))) + { +- mpfr_nexttozero (a); ++ if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ mpfr_setmax (a, __gmpfr_emax); ++ else ++ mpfr_nexttozero (a); + inexact = -MPFR_INT_SIGN (a); + } ++ else if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a)); + MPFR_RET (inexact); + } + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-06-01 13:00:30.772711162 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p2"; ++ return "3.1.4-p3"; + } +diff -Naurd mpfr-3.1.4-a/tests/tsub.c mpfr-3.1.4-b/tests/tsub.c +--- mpfr-3.1.4-a/tests/tsub.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub.c 2016-06-01 13:00:30.760711326 +0000 +@@ -630,6 +630,135 @@ + } + } + ++static void ++check_max_almosteven (void) ++{ ++ mpfr_exp_t old_emin, old_emax; ++ mpfr_exp_t emin[2] = { MPFR_EMIN_MIN, -1000 }; ++ mpfr_exp_t emax[2] = { MPFR_EMAX_MAX, 1000 }; ++ int i; ++ ++ old_emin = mpfr_get_emin (); ++ old_emax = mpfr_get_emax (); ++ ++ for (i = 0; i < 2; i++) ++ { ++ mpfr_t a1, a2, b, c; ++ mpfr_prec_t p; ++ int neg, j, rnd; ++ ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ ++ p = MPFR_PREC_MIN + randlimb () % 70; ++ mpfr_init2 (a1, p); ++ mpfr_init2 (a2, p); ++ mpfr_init2 (b, p+1); ++ mpfr_init2 (c, MPFR_PREC_MIN); ++ ++ mpfr_setmax (b, 0); ++ mpfr_set_ui (c, 1, MPFR_RNDN); ++ ++ for (neg = 0; neg < 2; neg++) ++ { ++ for (j = 1; j >= 0; j--) ++ { ++ mpfr_set_exp (b, __gmpfr_emax - j); ++ RND_LOOP (rnd) ++ { ++ unsigned int flags1, flags2; ++ int inex1, inex2; ++ ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (rnd == MPFR_RNDN || MPFR_IS_LIKE_RNDZ (rnd, neg)) ++ { ++ inex1 = neg ? 1 : -1; ++ mpfr_setmax (a1, __gmpfr_emax - j); ++ } ++ else ++ { ++ inex1 = neg ? -1 : 1; ++ if (j == 0) ++ { ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ mpfr_set_inf (a1, 1); ++ } ++ else ++ { ++ mpfr_setmin (a1, __gmpfr_emax); ++ } ++ } ++ MPFR_SET_SIGN (a1, neg ? -1 : 1); ++ ++ mpfr_clear_flags (); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 1 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ ++ if (i == 0) ++ break; ++ ++ mpfr_clear_flags (); ++ set_emin (MPFR_EMIN_MIN); ++ set_emax (MPFR_EMAX_MAX); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ inex2 = mpfr_check_range (a2, inex2, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 2 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } /* j */ ++ ++ mpfr_neg (b, b, MPFR_RNDN); ++ mpfr_neg (c, c, MPFR_RNDN); ++ } /* neg */ ++ ++ mpfr_clears (a1, a2, b, c, (mpfr_ptr) 0); ++ } /* i */ ++ ++ set_emin (old_emin); ++ set_emax (old_emax); ++} ++ + #define TEST_FUNCTION test_sub + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -647,6 +776,7 @@ + check_rounding (); + check_diverse (); + check_inexact (); ++ check_max_almosteven (); + bug_ddefour (); + for (p=2; p<200; p++) + for (i=0; i<50; i++) +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-08-04 20:41:14.097592781 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-08-04 20:41:14.121592350 +0000 +@@ -0,0 +1 @@ ++c++11-compat +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-06-01 13:00:30.772711162 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-08-04 20:41:14.121592350 +0000 +@@ -1 +1 @@ +-3.1.4-p3 ++3.1.4-p4 +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-08-04 20:41:14.121592350 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p3" ++#define MPFR_VERSION_STRING "3.1.4-p4" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-06-01 13:00:30.772711162 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-08-04 20:41:14.121592350 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p3"; ++ return "3.1.4-p4"; + } +diff -Naurd mpfr-3.1.4-a/tests/tpow_z.c mpfr-3.1.4-b/tests/tpow_z.c +--- mpfr-3.1.4-a/tests/tpow_z.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tpow_z.c 2016-08-04 20:41:14.113592494 +0000 +@@ -26,7 +26,7 @@ + + #include "mpfr-test.h" + +-#define ERROR(str) do { printf("Error for "str"\n"); exit (1); } while (0) ++#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) + + static void + check_special (void) +diff -Naurd mpfr-3.1.4-a/tests/tset_si.c mpfr-3.1.4-b/tests/tset_si.c +--- mpfr-3.1.4-a/tests/tset_si.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tset_si.c 2016-08-04 20:41:14.113592494 +0000 +@@ -26,7 +26,7 @@ + + #include "mpfr-test.h" + +-#define ERROR(str) {printf("Error for "str"\n"); exit(1);} ++#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) + + static void + test_2exp (void) +diff -Naurd mpfr-3.1.4-a/tests/tset_sj.c mpfr-3.1.4-b/tests/tset_sj.c +--- mpfr-3.1.4-a/tests/tset_sj.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tset_sj.c 2016-08-04 20:41:14.113592494 +0000 +@@ -42,7 +42,7 @@ + + #else + +-#define ERROR(str) {printf("Error for "str"\n"); exit(1);} ++#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) + + static int + inexact_sign (int x) +diff -Naurd mpfr-3.1.4-a/tests/tsi_op.c mpfr-3.1.4-b/tests/tsi_op.c +--- mpfr-3.1.4-a/tests/tsi_op.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsi_op.c 2016-08-04 20:41:14.113592494 +0000 +@@ -26,14 +26,16 @@ + + #include "mpfr-test.h" + +-#define ERROR1(s, i, z, exp) \ +-{\ +- printf("Error for "s" and i=%d\n", i);\ +- printf("Expected %s\n", exp);\ +- printf("Got "); mpfr_out_str (stdout, 16, 0, z, MPFR_RNDN);\ +- putchar ('\n');\ +- exit(1);\ +-} ++#define ERROR1(s,i,z,exp) \ ++ do \ ++ { \ ++ printf ("Error for " s " and i=%d\n", i); \ ++ printf ("Expected %s\n", exp); \ ++ printf ("Got "); mpfr_out_str (stdout, 16, 0, z, MPFR_RNDN); \ ++ putchar ('\n'); \ ++ exit(1); \ ++ } \ ++ while (0) + + const struct { + const char * op1; diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb new file mode 100644 index 0000000000..cf2c3b0bdb --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb @@ -0,0 +1,22 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.07' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, +including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.1.0' +binutilsver = '2.27' +gccbinver = '%s-%s' % (gccver, binutilsver) + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccbinver), # includes both GCC and binutils + ('OpenMPI', '1.10.2', '', ('GCC', gccbinver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb new file mode 100644 index 0000000000..659a1fdf27 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +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': 'GCC', 'version': '6.1.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..78e9122ea4 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb @@ -0,0 +1,26 @@ +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': 'GCCcore', 'version': '6.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCCcore +builddependencies = [('binutils', '2.27', '', True)] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb new file mode 100644 index 0000000000..75a0bc06f7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.18' + +lapackver = '3.6.1' +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': '2016.07'} + +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="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb new file mode 100644 index 0000000000..ac26d4212f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.1.0-2.27'} + +sources = [SOURCELOWER_TAR_GZ] + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] + +dependencies = [('hwloc', '1.11.3')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] + +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 libs] + + ["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-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb new file mode 100644 index 0000000000..d057e2fbb3 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.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': '2016.07'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blassuff = '-LAPACK-3.6.1' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('gompi', '2016.07'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb new file mode 100644 index 0000000000..47a40a4035 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb @@ -0,0 +1,25 @@ +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': 'GCCcore', 'version': '6.1.0'} +toolchainopts = {'pic': True} + +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', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From a24c191fe8715a8b7e0ffc8a6821868f8f85b425 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Fri, 2 Sep 2016 14:18:30 +0100 Subject: [PATCH 356/701] missed numactl off list --- .../numactl/numactl-2.0.11-GCC-6.1.0-2.27.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.1.0-2.27.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.1.0-2.27.eb new file mode 100644 index 0000000000..b862023bd6 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.1.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +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': 'GCC', 'version': '6.1.0-2.27'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' -- GitLab From cefdbf777d5dd07e46b8c938b4fc8896ba9421a1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 2 Sep 2016 15:49:18 +0200 Subject: [PATCH 357/701] Fix download of ParaView --- .../p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb index 3fba0f0166..1b7e04902f 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb @@ -12,9 +12,7 @@ toolchainopts = {'pic': True, 'usempi': 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"] - -# patches = ['%(name)s-%(version)s_missingheader.patch'] +sources = ["ParaView-v%(version)s.tar.gz"] dependencies = [ ('X11', '20160819'), @@ -26,7 +24,7 @@ dependencies = [ ('Python', '2.7.12'), ] -builddependencies = [('CMake', '3.5.2')] +builddependencies = [('CMake', '3.6.1')] separate_build_dir = True -- GitLab From 39dbbf73496e54c6fbffc51c8333781dfbdd60f6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 2 Sep 2016 15:54:14 +0200 Subject: [PATCH 358/701] Bring libxml2/2.9.4 with Python in sync with the others --- .../l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb index c0c3697f83..d2e63d779b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb @@ -3,9 +3,8 @@ version = '2.9.4' versionsuffix = '-Python-%(pyver)s' 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': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} @@ -16,8 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - dependencies = [ ('zlib', '1.2.8'), ('Python', '2.7.12'), -- GitLab From 0e868adf2743f0bb9d90876ea6692bccbc85d909 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 2 Sep 2016 15:54:59 +0200 Subject: [PATCH 359/701] Still allow Tk but add comment --- easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb index 42a21bb5f7..9f0f36a46a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb @@ -18,8 +18,8 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - # We don't build Tkinter as it requires an X11 stack - # ('Tk', '8.6.5'), + # Be ware that this requires a full X11 stack + ('Tk', '8.6.5'), ('GMP', '6.1.1'), ('libffi', '3.2.1'), # OS dependency should be preferred if the os version is more recent then this version, -- GitLab From 5259648054aaa69961ef39f41c79c6d967db90d4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 2 Sep 2016 17:18:13 +0200 Subject: [PATCH 360/701] Add warning about Tk and X To build Tk, you need an X11 stack. All current python easyconfig need X11 to build. Follow up in https://github.com/hpcugent/easybuild-easyconfigs/issues/2261 --- .../easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb | 4 ++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 2 +- .../p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb | 1 + .../easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb | 1 + easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb | 1 + 62 files changed, 63 insertions(+), 39 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb index c19c897045..fd80fddc40 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack # ('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-2.7.10-GNU-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb index 094f5e83b0..6e9aa1f7c4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack # ('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-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 2110e24871..1d651d49d1 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto # ('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 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index 76db705ebd..2247b6ef92 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # required for pycrypto # ('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 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb index a5549be298..74123d2915 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack # ('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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb index 1156ffc2af..803575d935 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.7.2')), # required for pycrypto # ('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 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb index 56b2274143..894b701f69 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.8.4')), # required for pycrypto # ('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 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 2661d5c96a..3d970938c9 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 @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto # ('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 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index 94c61afabc..8b5d70e944 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack # ('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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb index 9a52c8f87d..d69b594b08 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -26,7 +26,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb index 99f60636cb..ab13993dcf 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb @@ -26,7 +26,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb index 895d73b128..78953148b0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb @@ -19,7 +19,7 @@ dependencies = [ ('libreadline', '6.3', '', ('GCCcore', '4.9.3')), ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack # ('OpenSSL', '1.0.1q'), # 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-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index c4aea6d0fc..c5fe86070e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.10.0'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # required for pycrypto # ('OpenSSL', '1.0.1q'), # 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-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 3e1f1e63c6..cd19e3b902 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # 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-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index 5bee9397c4..917a362739 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # 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-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb index 98314b77b5..974e57d87c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -21,8 +21,8 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - #('Tk', '8.6.4', '-no-X11'), - ('Tk', '8.6.4'), + #('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack + ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # 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-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index 71a4890e47..fa2f05cdb9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # 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-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb index bb7d002230..914f184b70 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # 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-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 8ab42a8b9f..711240b058 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # 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-2.7.12-GCC-5.4.0-2.26-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb index fb337a3d58..abfcbbf934 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('Tk', '8.6.5'), # this requires a full X11 stack ('GMP', '6.1.1'), ('libffi', '3.2.1'), # OS dependency should be preferred if the os version is more recent then this version, diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb index 8bb576da7d..ba6ada1467 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('Tk', '8.6.5'), # this requires a full X11 stack ('GMP', '6.1.1'), ('libffi', '3.2.1'), # OS dependency should be preferred if the os version is more recent then this version, diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb index e77dca8172..f39ab1c056 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('Tk', '8.6.5'), # this requires a full X11 stack ('GMP', '6.1.1'), ('libffi', '3.2.1'), # OS dependency should be preferred if the os version is more recent then this version, 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 3b6c965221..a2e4addace 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', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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 75386ccc4a..f6e75ecf53 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', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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 a04b4992d3..e9063410df 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', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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 4d8258d281..d693b53480 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', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb index 81bfd4da01..62fde498fb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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 e8eb88c738..c78274679f 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', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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 7739e8b255..39cc28b030 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', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index 70860e49fa..fc6fced509 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index 41e6d0cc85..09da0c6f20 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'), - ('Tk', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack #('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 f327891d4e..c672a429fd 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', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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 188046b969..82f1c9fdc5 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', '8.6.3', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack # ('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-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index 6b562baa0c..40ab1396ff 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1p'), # 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-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index c11711336f..c0d918fab2 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index f0600eefc0..bb39588cab 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb index a637288eb8..33f145a36c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('Tk', '8.6.5'), # this requires a full X11 stack ('GMP', '6.1.1'), ('XZ', '5.2.2'), ('libffi', '3.2.1'), diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb index 46d7ae7573..4cba8641bb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), + ('Tk', '8.6.5'), # this requires a full X11 stack ('GMP', '6.1.1'), ('XZ', '5.2.2'), ('libffi', '3.2.1'), diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb index 878cfecf53..df6346fdf8 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb index ac0d5ff0bc..2394a09815 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb index 0cf00324c8..89e750afa3 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb index aaa247a658..fd29c33762 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015b-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb index 0a860475e3..be1ac13f46 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb index 890bfc8cfe..d5880a0b40 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb index b383831c92..3fa9a76738 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.16-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb index 6550c8a427..dccd1a9e2f 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb index 4762abfa09..68317abed0 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -18,6 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb index 75434aa7b8..02c810f4e3 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb @@ -19,6 +19,7 @@ dependencies = [ ('Tcl', version), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb index ce3ef51b8f..f156bb1a1b 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb @@ -19,6 +19,7 @@ dependencies = [ ('Tcl', version), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb index 684f3bddb6..8a30be2061 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.3-2.25-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb index f077e32cc2..50d6e63455 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x' start_dir = 'unix' 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 index 9e3efc89f0..2c44f99045 100644 --- 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 @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb index 89ecb3248a..9f80c4ee63 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb index 449ce63a29..57e512249b 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2016a-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8') ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb index 5066a5847c..be28b60358 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gimkl-2.11.5-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb index 9419fc66d6..a88315f807 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' 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 index 60f899a584..26804627ae 100644 --- 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 @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' 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 index 53f70e54d2..3e9e1cab39 100644 --- 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 @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' 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 85504f8688..ff4e4051ee 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 @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb index b7e6c77202..389d3ddf98 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb index ed76be27b6..873aa2d811 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016.02-GCC-4.9-no-X11.eb @@ -19,6 +19,7 @@ dependencies = [ ('Tcl', version), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb index 9eede49210..3174f88f27 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb @@ -20,6 +20,7 @@ dependencies = [ ('zlib', '1.2.8'), ] +# To be clear: this will still require X11 to be present (see issue #2261) configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' -- GitLab From 8240062fa77b301b1ad4ec9f6922569013579772 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 2 Sep 2016 17:21:00 +0200 Subject: [PATCH 361/701] Drop comments about X11, moved to #3519 --- easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb | 1 - easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb index 9f0f36a46a..e77dca8172 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb @@ -18,7 +18,6 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.13.0'), - # Be ware that this requires a full X11 stack ('Tk', '8.6.5'), ('GMP', '6.1.1'), ('libffi', '3.2.1'), diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb index ee021a1cfc..9eede49210 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2016a-no-X11.eb @@ -20,7 +20,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -# To be clear: this will still require the X11 to be present. configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' start_dir = 'unix' -- GitLab From 1144223127bd4f686c64d208d4309b4541dab951 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Fri, 2 Sep 2016 16:48:40 +0100 Subject: [PATCH 362/701] Removed hard-coded dep --- ...caLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb index d057e2fbb3..5345e93313 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-OpenBLAS-0.2.18-LAPACK-3.6.1.eb @@ -17,7 +17,7 @@ blassuff = '-LAPACK-3.6.1' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -dependencies = [(blaslib, blasver, blassuff, ('gompi', '2016.07'))] +dependencies = [(blaslib, blasver, blassuff)] # parallel build tends to fail, so disabling it parallel = 1 -- GitLab From a8bc587031ae47cb1cec474f478c899de220750e Mon Sep 17 00:00:00 2001 From: Appmaint Date: Sat, 3 Sep 2016 11:15:24 +0100 Subject: [PATCH 363/701] Made requested changes Changed Open MPI version to 1.10.3, removed duplicate patch, removed mirror link and fixed some style issues. --- easybuild/easyconfigs/f/foss/foss-2016.07.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 4 +- ...6.1.0_mpfr-3.1.4-allpatches-20160804.patch | 455 ------------------ .../easyconfigs/g/gompi/gompi-2016.07.eb | 2 +- .../OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb | 33 ++ 6 files changed, 38 insertions(+), 460 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_mpfr-3.1.4-allpatches-20160804.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2016.07.eb b/easybuild/easyconfigs/f/foss/foss-2016.07.eb index f4211bb9f3..052846a744 100644 --- a/easybuild/easyconfigs/f/foss/foss-2016.07.eb +++ b/easybuild/easyconfigs/f/foss/foss-2016.07.eb @@ -28,7 +28,7 @@ comp_mpi_tc = (comp_mpi_tc_name, version) # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ ('GCC', gccbinver), - ('OpenMPI', '1.10.2', '', ('GCC', gccbinver)), + ('OpenMPI', '1.10.3', '', ('GCC', gccbinver)), (blaslib, blasver, blassuff, comp_mpi_tc), ('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-6.1.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb index 258248286e..4faa0a48e8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb @@ -4,7 +4,7 @@ name = 'GCC' version = '6.1.0' binutilsver = '2.27' -versionsuffix = '-%s' % (binutilsver) +versionsuffix = '-%s' % binutilsver homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index d15501829b..456f0e7ef2 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -17,8 +17,8 @@ source_urls = [ '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 - 'http://ftp.heanet.ie/mirrors/gnu/%(namelower)s/%(namelower)s-%(version)s/', # Alternative for GCC 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://ftp.gnu.org/gnu/gcc/gcc-%(version)s/', # Alternative GCC ] sources = [ @@ -35,7 +35,7 @@ builddependencies = [ ] patches = [ - ('%s-%s_mpfr-%s-allpatches-20160804.patch' % (name, version, mpfr_version), '../mpfr-%s' % mpfr_version), + ('mpfr-%s-allpatches-20160804.patch' % (name, version, mpfr_version), '../mpfr-%s' % mpfr_version), ('%s-%s_fix-find-isl.patch' % (name, version)), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_mpfr-3.1.4-allpatches-20160804.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_mpfr-3.1.4-allpatches-20160804.patch deleted file mode 100644 index 41748b0345..0000000000 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0_mpfr-3.1.4-allpatches-20160804.patch +++ /dev/null @@ -1,455 +0,0 @@ -# All mpfr patches as of 2016-08-04, from same pull request for GCC 6.2.0 -# taken from their website: http://www.mpfr.org/mpfr-current/#download -diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES ---- mpfr-3.1.4-a/PATCHES 2016-04-13 21:22:23.720604013 +0000 -+++ mpfr-3.1.4-b/PATCHES 2016-04-13 21:22:23.744603677 +0000 -@@ -0,0 +1 @@ -+unix-check -diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION ---- mpfr-3.1.4-a/VERSION 2016-03-06 11:33:04.000000000 +0000 -+++ mpfr-3.1.4-b/VERSION 2016-04-13 21:22:23.744603677 +0000 -@@ -1 +1 @@ --3.1.4 -+3.1.4-p1 -diff -Naurd mpfr-3.1.4-a/src/mpfr-impl.h mpfr-3.1.4-b/src/mpfr-impl.h ---- mpfr-3.1.4-a/src/mpfr-impl.h 2016-03-06 11:33:04.000000000 +0000 -+++ mpfr-3.1.4-b/src/mpfr-impl.h 2016-04-13 21:22:23.736603789 +0000 -@@ -252,19 +252,6 @@ - # define MPFR_WIN_THREAD_SAFE_DLL 1 - #endif - --/* Detect some possible inconsistencies under Unix. */ --#if defined(__unix__) --# if defined(_WIN32) --# error "Both __unix__ and _WIN32 are defined" --# endif --# if __GMP_LIBGMP_DLL --# error "__unix__ is defined and __GMP_LIBGMP_DLL is true" --# endif --# if defined(MPFR_WIN_THREAD_SAFE_DLL) --# error "Both __unix__ and MPFR_WIN_THREAD_SAFE_DLL are defined" --# endif --#endif -- - #if defined(__MPFR_WITHIN_MPFR) || !defined(MPFR_WIN_THREAD_SAFE_DLL) - extern MPFR_THREAD_ATTR unsigned int __gmpfr_flags; - extern MPFR_THREAD_ATTR mpfr_exp_t __gmpfr_emin; -diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h ---- mpfr-3.1.4-a/src/mpfr.h 2016-03-06 11:33:04.000000000 +0000 -+++ mpfr-3.1.4-b/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 -@@ -27,7 +27,7 @@ - #define MPFR_VERSION_MAJOR 3 - #define MPFR_VERSION_MINOR 1 - #define MPFR_VERSION_PATCHLEVEL 4 --#define MPFR_VERSION_STRING "3.1.4" -+#define MPFR_VERSION_STRING "3.1.4-p1" - - /* Macros dealing with MPFR VERSION */ - #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) -diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c ---- mpfr-3.1.4-a/src/version.c 2016-03-06 11:33:05.000000000 +0000 -+++ mpfr-3.1.4-b/src/version.c 2016-04-13 21:22:23.744603677 +0000 -@@ -25,5 +25,5 @@ - const char * - mpfr_get_version (void) - { -- return "3.1.4"; -+ return "3.1.4-p1"; - } -diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES ---- mpfr-3.1.4-a/PATCHES 2016-05-22 19:59:43.838399677 +0000 -+++ mpfr-3.1.4-b/PATCHES 2016-05-22 19:59:43.866399168 +0000 -@@ -0,0 +1 @@ -+add-sub-ui-flags -diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION ---- mpfr-3.1.4-a/VERSION 2016-04-13 21:22:23.744603677 +0000 -+++ mpfr-3.1.4-b/VERSION 2016-05-22 19:59:43.866399168 +0000 -@@ -1 +1 @@ --3.1.4-p1 -+3.1.4-p2 -diff -Naurd mpfr-3.1.4-a/src/add_ui.c mpfr-3.1.4-b/src/add_ui.c ---- mpfr-3.1.4-a/src/add_ui.c 2016-03-06 11:33:04.000000000 +0000 -+++ mpfr-3.1.4-b/src/add_ui.c 2016-05-22 19:59:43.854399385 +0000 -@@ -49,6 +49,7 @@ - MPFR_SAVE_EXPO_MARK (expo); - MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); - inex = mpfr_add(y, x, uu, rnd_mode); -+ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); - MPFR_SAVE_EXPO_FREE (expo); - return mpfr_check_range(y, inex, rnd_mode); - } -diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h ---- mpfr-3.1.4-a/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 -+++ mpfr-3.1.4-b/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 -@@ -27,7 +27,7 @@ - #define MPFR_VERSION_MAJOR 3 - #define MPFR_VERSION_MINOR 1 - #define MPFR_VERSION_PATCHLEVEL 4 --#define MPFR_VERSION_STRING "3.1.4-p1" -+#define MPFR_VERSION_STRING "3.1.4-p2" - - /* Macros dealing with MPFR VERSION */ - #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) -diff -Naurd mpfr-3.1.4-a/src/sub_ui.c mpfr-3.1.4-b/src/sub_ui.c ---- mpfr-3.1.4-a/src/sub_ui.c 2016-03-06 11:33:05.000000000 +0000 -+++ mpfr-3.1.4-b/src/sub_ui.c 2016-05-22 19:59:43.854399385 +0000 -@@ -52,6 +52,7 @@ - MPFR_SAVE_EXPO_MARK (expo); - MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); - inex = mpfr_sub (y, x, uu, rnd_mode); -+ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); - MPFR_SAVE_EXPO_FREE (expo); - return mpfr_check_range (y, inex, rnd_mode); - } -diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c ---- mpfr-3.1.4-a/src/version.c 2016-04-13 21:22:23.744603677 +0000 -+++ mpfr-3.1.4-b/src/version.c 2016-05-22 19:59:43.866399168 +0000 -@@ -25,5 +25,5 @@ - const char * - mpfr_get_version (void) - { -- return "3.1.4-p1"; -+ return "3.1.4-p2"; - } -diff -Naurd mpfr-3.1.4-a/tests/tadd_ui.c mpfr-3.1.4-b/tests/tadd_ui.c ---- mpfr-3.1.4-a/tests/tadd_ui.c 2016-03-06 11:33:03.000000000 +0000 -+++ mpfr-3.1.4-b/tests/tadd_ui.c 2016-05-22 19:59:43.854399385 +0000 -@@ -69,7 +69,9 @@ - - /* nan + 2394875 == nan */ - mpfr_set_nan (x); -+ mpfr_clear_nanflag (); - mpfr_add_ui (y, x, 2394875L, MPFR_RNDN); -+ MPFR_ASSERTN (mpfr_nanflag_p ()); - MPFR_ASSERTN (mpfr_nan_p (y)); - - /* +inf + 2394875 == +inf */ -diff -Naurd mpfr-3.1.4-a/tests/tsub_ui.c mpfr-3.1.4-b/tests/tsub_ui.c ---- mpfr-3.1.4-a/tests/tsub_ui.c 2016-03-06 11:33:03.000000000 +0000 -+++ mpfr-3.1.4-b/tests/tsub_ui.c 2016-05-22 19:59:43.854399385 +0000 -@@ -96,7 +96,9 @@ - - /* nan - 1 == nan */ - mpfr_set_nan (x); -+ mpfr_clear_nanflag (); - mpfr_sub_ui (y, x, 1L, MPFR_RNDN); -+ MPFR_ASSERTN (mpfr_nanflag_p ()); - MPFR_ASSERTN (mpfr_nan_p (y)); - - /* +inf - 1 == +inf */ -diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES ---- mpfr-3.1.4-a/PATCHES 2016-06-01 13:00:30.748711490 +0000 -+++ mpfr-3.1.4-b/PATCHES 2016-06-01 13:00:30.772711162 +0000 -@@ -0,0 +1 @@ -+sub1-overflow -diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION ---- mpfr-3.1.4-a/VERSION 2016-05-22 19:59:43.866399168 +0000 -+++ mpfr-3.1.4-b/VERSION 2016-06-01 13:00:30.772711162 +0000 -@@ -1 +1 @@ --3.1.4-p2 -+3.1.4-p3 -diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h ---- mpfr-3.1.4-a/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 -+++ mpfr-3.1.4-b/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 -@@ -27,7 +27,7 @@ - #define MPFR_VERSION_MAJOR 3 - #define MPFR_VERSION_MINOR 1 - #define MPFR_VERSION_PATCHLEVEL 4 --#define MPFR_VERSION_STRING "3.1.4-p2" -+#define MPFR_VERSION_STRING "3.1.4-p3" - - /* Macros dealing with MPFR VERSION */ - #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) -diff -Naurd mpfr-3.1.4-a/src/sub1.c mpfr-3.1.4-b/src/sub1.c ---- mpfr-3.1.4-a/src/sub1.c 2016-03-06 11:33:05.000000000 +0000 -+++ mpfr-3.1.4-b/src/sub1.c 2016-06-01 13:00:30.760711326 +0000 -@@ -96,16 +96,15 @@ - /* A = S*ABS(B) +/- ulp(a) */ - MPFR_SET_EXP (a, MPFR_GET_EXP (b)); - MPFR_RNDRAW_EVEN (inexact, a, MPFR_MANT (b), MPFR_PREC (b), -- rnd_mode, MPFR_SIGN (a), -- if (MPFR_UNLIKELY ( ++MPFR_EXP (a) > __gmpfr_emax)) -- inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a))); -- /* inexact = mpfr_set4 (a, b, rnd_mode, MPFR_SIGN (a)); */ -+ rnd_mode, MPFR_SIGN (a), ++ MPFR_EXP (a)); - if (inexact == 0) - { - /* a = b (Exact) - But we know it isn't (Since we have to remove `c') - So if we round to Zero, we have to remove one ulp. - Otherwise the result is correctly rounded. */ -+ /* An overflow is not possible. */ -+ MPFR_ASSERTD (MPFR_EXP (a) <= __gmpfr_emax); - if (MPFR_IS_LIKE_RNDZ (rnd_mode, MPFR_IS_NEG (a))) - { - mpfr_nexttozero (a); -@@ -136,9 +135,14 @@ - i.e. inexact= MPFR_EVEN_INEX */ - if (MPFR_UNLIKELY (inexact == MPFR_EVEN_INEX*MPFR_INT_SIGN (a))) - { -- mpfr_nexttozero (a); -+ if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) -+ mpfr_setmax (a, __gmpfr_emax); -+ else -+ mpfr_nexttozero (a); - inexact = -MPFR_INT_SIGN (a); - } -+ else if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) -+ inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a)); - MPFR_RET (inexact); - } - } -diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c ---- mpfr-3.1.4-a/src/version.c 2016-05-22 19:59:43.866399168 +0000 -+++ mpfr-3.1.4-b/src/version.c 2016-06-01 13:00:30.772711162 +0000 -@@ -25,5 +25,5 @@ - const char * - mpfr_get_version (void) - { -- return "3.1.4-p2"; -+ return "3.1.4-p3"; - } -diff -Naurd mpfr-3.1.4-a/tests/tsub.c mpfr-3.1.4-b/tests/tsub.c ---- mpfr-3.1.4-a/tests/tsub.c 2016-03-06 11:33:03.000000000 +0000 -+++ mpfr-3.1.4-b/tests/tsub.c 2016-06-01 13:00:30.760711326 +0000 -@@ -630,6 +630,135 @@ - } - } - -+static void -+check_max_almosteven (void) -+{ -+ mpfr_exp_t old_emin, old_emax; -+ mpfr_exp_t emin[2] = { MPFR_EMIN_MIN, -1000 }; -+ mpfr_exp_t emax[2] = { MPFR_EMAX_MAX, 1000 }; -+ int i; -+ -+ old_emin = mpfr_get_emin (); -+ old_emax = mpfr_get_emax (); -+ -+ for (i = 0; i < 2; i++) -+ { -+ mpfr_t a1, a2, b, c; -+ mpfr_prec_t p; -+ int neg, j, rnd; -+ -+ set_emin (emin[i]); -+ set_emax (emax[i]); -+ -+ p = MPFR_PREC_MIN + randlimb () % 70; -+ mpfr_init2 (a1, p); -+ mpfr_init2 (a2, p); -+ mpfr_init2 (b, p+1); -+ mpfr_init2 (c, MPFR_PREC_MIN); -+ -+ mpfr_setmax (b, 0); -+ mpfr_set_ui (c, 1, MPFR_RNDN); -+ -+ for (neg = 0; neg < 2; neg++) -+ { -+ for (j = 1; j >= 0; j--) -+ { -+ mpfr_set_exp (b, __gmpfr_emax - j); -+ RND_LOOP (rnd) -+ { -+ unsigned int flags1, flags2; -+ int inex1, inex2; -+ -+ flags1 = MPFR_FLAGS_INEXACT; -+ if (rnd == MPFR_RNDN || MPFR_IS_LIKE_RNDZ (rnd, neg)) -+ { -+ inex1 = neg ? 1 : -1; -+ mpfr_setmax (a1, __gmpfr_emax - j); -+ } -+ else -+ { -+ inex1 = neg ? -1 : 1; -+ if (j == 0) -+ { -+ flags1 |= MPFR_FLAGS_OVERFLOW; -+ mpfr_set_inf (a1, 1); -+ } -+ else -+ { -+ mpfr_setmin (a1, __gmpfr_emax); -+ } -+ } -+ MPFR_SET_SIGN (a1, neg ? -1 : 1); -+ -+ mpfr_clear_flags (); -+ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); -+ flags2 = __gmpfr_flags; -+ -+ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && -+ mpfr_equal_p (a1, a2))) -+ { -+ printf ("Error 1 in check_max_almosteven for %s," -+ " i = %d, j = %d, neg = %d\n", -+ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), -+ i, j, neg); -+ printf (" b = "); -+ mpfr_dump (b); -+ printf ("Expected "); -+ mpfr_dump (a1); -+ printf (" with inex = %d, flags =", inex1); -+ flags_out (flags1); -+ printf ("Got "); -+ mpfr_dump (a2); -+ printf (" with inex = %d, flags =", inex2); -+ flags_out (flags2); -+ exit (1); -+ } -+ -+ if (i == 0) -+ break; -+ -+ mpfr_clear_flags (); -+ set_emin (MPFR_EMIN_MIN); -+ set_emax (MPFR_EMAX_MAX); -+ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); -+ set_emin (emin[i]); -+ set_emax (emax[i]); -+ inex2 = mpfr_check_range (a2, inex2, (mpfr_rnd_t) rnd); -+ flags2 = __gmpfr_flags; -+ -+ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && -+ mpfr_equal_p (a1, a2))) -+ { -+ printf ("Error 2 in check_max_almosteven for %s," -+ " i = %d, j = %d, neg = %d\n", -+ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), -+ i, j, neg); -+ printf (" b = "); -+ mpfr_dump (b); -+ printf ("Expected "); -+ mpfr_dump (a1); -+ printf (" with inex = %d, flags =", inex1); -+ flags_out (flags1); -+ printf ("Got "); -+ mpfr_dump (a2); -+ printf (" with inex = %d, flags =", inex2); -+ flags_out (flags2); -+ exit (1); -+ } -+ } -+ } /* j */ -+ -+ mpfr_neg (b, b, MPFR_RNDN); -+ mpfr_neg (c, c, MPFR_RNDN); -+ } /* neg */ -+ -+ mpfr_clears (a1, a2, b, c, (mpfr_ptr) 0); -+ } /* i */ -+ -+ set_emin (old_emin); -+ set_emax (old_emax); -+} -+ - #define TEST_FUNCTION test_sub - #define TWO_ARGS - #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) -@@ -647,6 +776,7 @@ - check_rounding (); - check_diverse (); - check_inexact (); -+ check_max_almosteven (); - bug_ddefour (); - for (p=2; p<200; p++) - for (i=0; i<50; i++) -diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES ---- mpfr-3.1.4-a/PATCHES 2016-08-04 20:41:14.097592781 +0000 -+++ mpfr-3.1.4-b/PATCHES 2016-08-04 20:41:14.121592350 +0000 -@@ -0,0 +1 @@ -+c++11-compat -diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION ---- mpfr-3.1.4-a/VERSION 2016-06-01 13:00:30.772711162 +0000 -+++ mpfr-3.1.4-b/VERSION 2016-08-04 20:41:14.121592350 +0000 -@@ -1 +1 @@ --3.1.4-p3 -+3.1.4-p4 -diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h ---- mpfr-3.1.4-a/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 -+++ mpfr-3.1.4-b/src/mpfr.h 2016-08-04 20:41:14.121592350 +0000 -@@ -27,7 +27,7 @@ - #define MPFR_VERSION_MAJOR 3 - #define MPFR_VERSION_MINOR 1 - #define MPFR_VERSION_PATCHLEVEL 4 --#define MPFR_VERSION_STRING "3.1.4-p3" -+#define MPFR_VERSION_STRING "3.1.4-p4" - - /* Macros dealing with MPFR VERSION */ - #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) -diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c ---- mpfr-3.1.4-a/src/version.c 2016-06-01 13:00:30.772711162 +0000 -+++ mpfr-3.1.4-b/src/version.c 2016-08-04 20:41:14.121592350 +0000 -@@ -25,5 +25,5 @@ - const char * - mpfr_get_version (void) - { -- return "3.1.4-p3"; -+ return "3.1.4-p4"; - } -diff -Naurd mpfr-3.1.4-a/tests/tpow_z.c mpfr-3.1.4-b/tests/tpow_z.c ---- mpfr-3.1.4-a/tests/tpow_z.c 2016-03-06 11:33:03.000000000 +0000 -+++ mpfr-3.1.4-b/tests/tpow_z.c 2016-08-04 20:41:14.113592494 +0000 -@@ -26,7 +26,7 @@ - - #include "mpfr-test.h" - --#define ERROR(str) do { printf("Error for "str"\n"); exit (1); } while (0) -+#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) - - static void - check_special (void) -diff -Naurd mpfr-3.1.4-a/tests/tset_si.c mpfr-3.1.4-b/tests/tset_si.c ---- mpfr-3.1.4-a/tests/tset_si.c 2016-03-06 11:33:03.000000000 +0000 -+++ mpfr-3.1.4-b/tests/tset_si.c 2016-08-04 20:41:14.113592494 +0000 -@@ -26,7 +26,7 @@ - - #include "mpfr-test.h" - --#define ERROR(str) {printf("Error for "str"\n"); exit(1);} -+#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) - - static void - test_2exp (void) -diff -Naurd mpfr-3.1.4-a/tests/tset_sj.c mpfr-3.1.4-b/tests/tset_sj.c ---- mpfr-3.1.4-a/tests/tset_sj.c 2016-03-06 11:33:03.000000000 +0000 -+++ mpfr-3.1.4-b/tests/tset_sj.c 2016-08-04 20:41:14.113592494 +0000 -@@ -42,7 +42,7 @@ - - #else - --#define ERROR(str) {printf("Error for "str"\n"); exit(1);} -+#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) - - static int - inexact_sign (int x) -diff -Naurd mpfr-3.1.4-a/tests/tsi_op.c mpfr-3.1.4-b/tests/tsi_op.c ---- mpfr-3.1.4-a/tests/tsi_op.c 2016-03-06 11:33:03.000000000 +0000 -+++ mpfr-3.1.4-b/tests/tsi_op.c 2016-08-04 20:41:14.113592494 +0000 -@@ -26,14 +26,16 @@ - - #include "mpfr-test.h" - --#define ERROR1(s, i, z, exp) \ --{\ -- printf("Error for "s" and i=%d\n", i);\ -- printf("Expected %s\n", exp);\ -- printf("Got "); mpfr_out_str (stdout, 16, 0, z, MPFR_RNDN);\ -- putchar ('\n');\ -- exit(1);\ --} -+#define ERROR1(s,i,z,exp) \ -+ do \ -+ { \ -+ printf ("Error for " s " and i=%d\n", i); \ -+ printf ("Expected %s\n", exp); \ -+ printf ("Got "); mpfr_out_str (stdout, 16, 0, z, MPFR_RNDN); \ -+ putchar ('\n'); \ -+ exit(1); \ -+ } \ -+ while (0) - - const struct { - const char * op1; diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb index cf2c3b0bdb..5eca4152c8 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb @@ -16,7 +16,7 @@ gccbinver = '%s-%s' % (gccver, binutilsver) # compiler toolchain dependencies dependencies = [ ('GCC', gccbinver), # includes both GCC and binutils - ('OpenMPI', '1.10.2', '', ('GCC', gccbinver)), + ('OpenMPI', '1.10.3', '', ('GCC', gccbinver)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb new file mode 100644 index 0000000000..af22c5f516 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.3' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.1.0-2.27'} + +sources = [SOURCELOWER_TAR_GZ] + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] + +dependencies = [('hwloc', '1.11.3')] + +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'),] + +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 libs] + + ["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 dfbfc0c60a0f645216c13ee4f1bba98544f0dd90 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Sat, 3 Sep 2016 11:27:56 +0100 Subject: [PATCH 364/701] Forgot to change string substitution args --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index 456f0e7ef2..5b9af4041a 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -35,7 +35,7 @@ builddependencies = [ ] patches = [ - ('mpfr-%s-allpatches-20160804.patch' % (name, version, mpfr_version), '../mpfr-%s' % mpfr_version), + ('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), ('%s-%s_fix-find-isl.patch' % (name, version)), ] -- GitLab From 31c24cd0326c0ffdbe2d2db7d3d6dd23e50f96e2 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Sat, 3 Sep 2016 11:36:57 +0100 Subject: [PATCH 365/701] HPL 2.2 test for foss 2016.07 --- .../easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb new file mode 100644 index 0000000000..c44018425b --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +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': '2016.07'} +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 09d50312c50fb2b2bae0634ece52e35088ff6a73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 3 Sep 2016 18:26:45 +0200 Subject: [PATCH 366/701] remove empty versionsuffix in Perl dep spec in YAML-Syck easyconfigs + use %(pyver)s --- .../YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb | 11 +++-------- .../YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb | 11 +++-------- .../YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb | 11 +++-------- 3 files changed, 9 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb index 04fcdaad37..32cee4cfcb 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb @@ -11,6 +11,7 @@ easyblock = 'PerlModule' name = 'YAML-Syck' version = '1.27' +versionsuffix = '-Perl-%(pyver)s' homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' description = """Fast, lightweight YAML loader and dumper. @@ -21,21 +22,15 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://www.cpan.org/modules/by-module/YAML'] sources = [SOURCE_TAR_GZ] -perl = 'Perl' -perlver = '5.16.3' -perlverextra = '' -versionsuffix = '-%s-%s%s' % (perl, perlver, perlverextra) - dependencies = [ - (perl, perlver, perlverextra), + ('Perl', '5.16.3'), ] options = {'modulename': 'YAML::Syck'} -perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/YAML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb index 814139aaa0..b18bdca8af 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb @@ -11,6 +11,7 @@ easyblock = 'PerlModule' name = 'YAML-Syck' version = '1.27' +versionsuffix = '-Perl-%(pyver)s' homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' description = """Fast, lightweight YAML loader and dumper. @@ -21,21 +22,15 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = ['http://www.cpan.org/modules/by-module/YAML'] sources = [SOURCE_TAR_GZ] -perl = 'Perl' -perlver = '5.16.3' -perlverextra = '' -versionsuffix = '-%s-%s%s' % (perl, perlver, perlverextra) - dependencies = [ - (perl, perlver, perlverextra), + ('Perl', '5.16.3'), ] options = {'modulename': 'YAML::Syck'} -perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/YAML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb index 4816f11ffd..3704ca4fad 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb @@ -11,6 +11,7 @@ easyblock = 'PerlModule' name = 'YAML-Syck' version = '1.27' +versionsuffix = '-Perl-%(pyver)s' homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' description = """Fast, lightweight YAML loader and dumper. @@ -21,21 +22,15 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://www.cpan.org/modules/by-module/YAML'] sources = [SOURCE_TAR_GZ] -perl = 'Perl' -perlver = '5.16.3' -perlverextra = '' -versionsuffix = '-%s-%s%s' % (perl, perlver, perlverextra) - dependencies = [ - (perl, perlver, perlverextra), + ('Perl', '5.16.3'), ] options = {'modulename': 'YAML::Syck'} -perlmajver = perlver.split('.')[0] sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/YAML'], } moduleclass = 'data' -- GitLab From bc6294bf4731c2db1d89d6f295ac4a861ba7cc3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 3 Sep 2016 18:28:15 +0200 Subject: [PATCH 367/701] significantly speed up verifying dumped easyconfig by resorting to 'shallow' parsing --- test/easyconfigs/easyconfigs.py | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 13ea1263cd..6fbaa4bb1d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -44,9 +44,10 @@ import easybuild.main as main import easybuild.tools.options as eboptions from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.framework.easyblock import EasyBlock +from easybuild.framework.easyconfig.default import DEFAULT_CONFIG from easybuild.framework.easyconfig.easyconfig import EasyConfig -from easybuild.framework.easyconfig.easyconfig import get_easyblock_class -from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig +from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, resolve_template +from easybuild.framework.easyconfig.parser import EasyConfigParser, 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.config import build_option @@ -269,7 +270,7 @@ def template_easyconfig_test(self, spec): os.close(handle) ec.dump(test_ecfile) - dumped_ec = EasyConfig(test_ecfile) + dumped_ec = EasyConfigParser(test_ecfile).get_config_dict() os.remove(test_ecfile) # inject dummy values for templates that are only known at a later stage @@ -278,10 +279,16 @@ def template_easyconfig_test(self, spec): '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]) + ec_dict = ec.parser.get_config_dict() + for key in sorted(ec_dict): + orig_val = resolve_template(ec_dict[key], ec.template_values) + if key not in DEFAULT_CONFIG or orig_val == DEFAULT_CONFIG[key][0]: + continue + + dumped_val = resolve_template(dumped_ec[key], ec.template_values) + + self.assertEqual(orig_val, dumped_val) # cache the parsed easyconfig, to avoid that it is parsed again self.parsed_easyconfigs.append(ecs[0]) -- GitLab From 4cd26594e8e30d1ad1aa04248ac74d7d165ad58b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 3 Sep 2016 19:09:39 +0200 Subject: [PATCH 368/701] use %(perlver)s rather than %(pyver)s in YAML-Syck easyconfigs --- .../y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb | 2 +- .../y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb | 2 +- .../y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb index 32cee4cfcb..8cae54960c 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb @@ -11,7 +11,7 @@ easyblock = 'PerlModule' name = 'YAML-Syck' version = '1.27' -versionsuffix = '-Perl-%(pyver)s' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' description = """Fast, lightweight YAML loader and dumper. diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb index b18bdca8af..5efafeb0f0 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb @@ -11,7 +11,7 @@ easyblock = 'PerlModule' name = 'YAML-Syck' version = '1.27' -versionsuffix = '-Perl-%(pyver)s' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' description = """Fast, lightweight YAML loader and dumper. diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb index 3704ca4fad..19442cc19e 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb @@ -11,7 +11,7 @@ easyblock = 'PerlModule' name = 'YAML-Syck' version = '1.27' -versionsuffix = '-Perl-%(pyver)s' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' description = """Fast, lightweight YAML loader and dumper. -- GitLab From 6e8437fb7ad0382dbf0245f7d3f8730388373a20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 4 Sep 2016 22:47:06 +0200 Subject: [PATCH 369/701] fix checking of dumped easyconfig --- test/easyconfigs/easyconfigs.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 6fbaa4bb1d..3deb2e88ee 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -259,7 +259,8 @@ def template_easyconfig_test(self, spec): self.assertTrue(os.path.isfile(ext_patch_full), msg) # check whether all extra_options defined for used easyblock are defined - for key in app.extra_options(): + extra_opts = app.extra_options() + for key in extra_opts: self.assertTrue(key in app.cfg) app.close_log() @@ -281,11 +282,19 @@ def template_easyconfig_test(self, spec): ec.template_values.update(dummy_template_values) ec_dict = ec.parser.get_config_dict() - for key in sorted(ec_dict): - orig_val = resolve_template(ec_dict[key], ec.template_values) - if key not in DEFAULT_CONFIG or orig_val == DEFAULT_CONFIG[key][0]: + keys = [] + for key in ec_dict: + # skip parameters for which value is equal to default value + orig_val = ec_dict[key] + if key in DEFAULT_CONFIG and orig_val == DEFAULT_CONFIG[key][0]: + continue + if key in extra_opts and orig_val == extra_opts[key][0]: + continue + if key not in DEFAULT_CONFIG and key not in extra_opts: continue + keys.append(key) + orig_val = resolve_template(ec_dict[key], ec.template_values) dumped_val = resolve_template(dumped_ec[key], ec.template_values) self.assertEqual(orig_val, dumped_val) @@ -296,6 +305,7 @@ def template_easyconfig_test(self, spec): # test passed, so set back to True single_tests_ok = True and prev_single_tests_ok + def suite(): """Return all easyblock initialisation tests.""" # dynamically generate a separate test for each of the available easyconfigs -- GitLab From 8aa6003c44e14452dfdbe331b0b3fe1ae221e62a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 5 Sep 2016 11:42:30 +0200 Subject: [PATCH 370/701] METIS: use doubles instead of floats by default --- ...0-intel-2016b-32bitIDX.eb => METIS-5.1.0-intel-2016b.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/m/METIS/{METIS-5.1.0-intel-2016b-32bitIDX.eb => METIS-5.1.0-intel-2016b.eb} (86%) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b-32bitIDX.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.eb similarity index 86% rename from easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b-32bitIDX.eb rename to easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.eb index 9c8e6cc340..75f09a7d43 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b-32bitIDX.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.eb @@ -1,7 +1,5 @@ name = 'METIS' version = '5.1.0' -# default 32-bit IDTYPEWIDTH, no patch used -versionsuffix = '-32bitIDX' 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, @@ -17,7 +15,9 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] -builddependencies = [('CMake', '3.5.2')] +patches = ['METIS-5.1.0-use-doubles.patch'] + +builddependencies = [('CMake', '3.6.1')] configopts = ['', 'shared=1'] -- GitLab From f02f59791109924cce105d13736009bc4ed0c6c5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 5 Sep 2016 13:18:34 +0200 Subject: [PATCH 371/701] Fix OpenFOAM patches and METIS What's new: we don't need the Third Party stuff anymore, it's all EB now. --- .../o/OpenFOAM/OpenFOAM-4.0-cleanup.patch | 291 ++++++++++++++++++ 1 file changed, 291 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch new file mode 100644 index 0000000000..1afeb16c3a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch @@ -0,0 +1,291 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# Ward Poelmans +diff -ur OpenFOAM-4.0.orig/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-4.0/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-4.0.orig/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-09-02 15:44:36.305512075 +0200 +@@ -9,11 +9,11 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo "Found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" +- export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ur OpenFOAM-4.0.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-4.0/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-4.0.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-09-02 15:44:36.305512075 +0200 +@@ -16,7 +16,7 @@ + } + + # ensure CMake gets the correct C++ compiler +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVReaders + PVblockMeshReader/Allwmake $* +diff -ur OpenFOAM-4.0.orig/etc/bashrc OpenFOAM-4.0/etc/bashrc +--- OpenFOAM-4.0.orig/etc/bashrc 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/bashrc 2016-09-02 15:43:37.773220097 +0200 +@@ -42,9 +42,8 @@ + # + # Please set to the appropriate path if the default is not correct. + # +-[ $BASH_SOURCE ] && \ +-export FOAM_INST_DIR=${BASH_SOURCE%/*/*/*} || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module ++# + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ur OpenFOAM-4.0.orig/etc/config.sh/CGAL OpenFOAM-4.0/etc/config.sh/CGAL +--- OpenFOAM-4.0.orig/etc/config.sh/CGAL 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/CGAL 2016-09-02 15:43:37.773220097 +0200 +@@ -36,37 +36,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=cgal-system +-#cgal_version=CGAL-4.8 +- +-if [ -z "$SOURCE_CGAL_VERSIONS_ONLY" ] +-then +- +- common_path=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +- export BOOST_ARCH_PATH=$common_path/$boost_version +- export CGAL_ARCH_PATH=$common_path/$cgal_version +- +- if [ "$FOAM_VERBOSE" -a "$PS1" ] +- then +- echo "Using CGAL and boost" 1>&2 +- echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2 +- echo " $boost_version at $BOOST_ARCH_PATH" 1>&2 +- fi +- +- if [ -d "$CGAL_ARCH_PATH" -a "$cgal_version" != "cgal-system" ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib +- fi +- +- if [ -d "$BOOST_ARCH_PATH" -a "$boost_version" != "boost-system" ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib +- fi +- +- unset boost_version cgal_version common_path +- +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.0.orig/etc/config.sh/gperftools OpenFOAM-4.0/etc/config.sh/gperftools +--- OpenFOAM-4.0.orig/etc/config.sh/gperftools 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/gperftools 2016-09-02 15:43:37.773220097 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.0.orig/etc/config.sh/metis OpenFOAM-4.0/etc/config.sh/metis +--- OpenFOAM-4.0.orig/etc/config.sh/metis 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/metis 2016-09-02 15:43:37.773220097 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.0.orig/etc/config.sh/mpi OpenFOAM-4.0/etc/config.sh/mpi +--- OpenFOAM-4.0.orig/etc/config.sh/mpi 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/mpi 2016-09-02 15:43:37.773220097 +0200 +@@ -243,6 +243,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ur OpenFOAM-4.0.orig/etc/config.sh/paraview OpenFOAM-4.0/etc/config.sh/paraview +--- OpenFOAM-4.0.orig/etc/config.sh/paraview 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/paraview 2016-09-02 15:43:37.773220097 +0200 +@@ -41,21 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \ +- cmake-2.8.1 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 +@@ -64,7 +49,7 @@ + #export ParaView_VERSION=4.3.1 + #export ParaView_VERSION=4.4.0 + #export ParaView_VERSION=5.0.0 +-export ParaView_VERSION=5.0.1 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + +@@ -105,21 +90,15 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # Set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] + then + export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview-3.0 ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-3.0 +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -131,17 +110,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ur OpenFOAM-4.0.orig/etc/config.sh/scotch OpenFOAM-4.0/etc/config.sh/scotch +--- OpenFOAM-4.0.orig/etc/config.sh/scotch 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/scotch 2016-09-02 15:43:37.773220097 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.0.orig/etc/config.sh/settings OpenFOAM-4.0/etc/config.sh/settings +--- OpenFOAM-4.0.orig/etc/config.sh/settings 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/etc/config.sh/settings 2016-09-02 15:43:37.773220097 +0200 +@@ -56,11 +56,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$I_MPI_CC ++ export WM_CXX=$I_MPI_CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ur OpenFOAM-4.0.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-4.0/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-4.0.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/src/parallel/decompose/ptscotchDecomp/Make/options 2016-09-02 15:44:36.305512075 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ur OpenFOAM-4.0.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-4.0/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-4.0.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-09-02 15:45:13.376950242 +0200 +@@ -30,10 +30,11 @@ + #include "globalIndex.H" + #include "SubField.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ur OpenFOAM-4.0.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-4.0/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-4.0.orig/src/parallel/decompose/scotchDecomp/Make/options 2016-06-24 23:33:52.000000000 +0200 ++++ OpenFOAM-4.0/src/parallel/decompose/scotchDecomp/Make/options 2016-09-02 15:44:36.305512075 +0200 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt -- GitLab From d70d75cac6ecf305b9eb547fcd18233496d18426 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 5 Sep 2016 13:19:29 +0200 Subject: [PATCH 372/701] Now with actual changes from last commit --- .../m/METIS/METIS-5.1.0-intel-2016b.eb | 1 + .../o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb | 29 +++++++------------ 2 files changed, 11 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.eb index 75f09a7d43..65e2ae532f 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2016b.eb @@ -15,6 +15,7 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] +# We use 32bit for indices and 64bit for content patches = ['METIS-5.1.0-use-doubles.patch'] builddependencies = [('CMake', '3.6.1')] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb index 0caa9fc8da..635072f873 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb @@ -10,35 +10,26 @@ description = """OpenFOAM is a free, open source CFD software package. toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'cstd': 'c++11'} -source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] -sources = [ - SOURCE_TGZ, - 'ThirdParty-%(version)s.tgz', -] +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] -paraversion = '5.1.2' -patches = [ - 'OpenFOAM-%(version)s_cleanup.patch', - 'OpenFOAM-%(version)s_libreadline.patch', - ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir - 'OpenFOAM-%(version)s_external-3rd.patch', - ('ThirdParty-%(version)s_external-3rd.patch', ".."), - 'OpenFOAM-%%(version)s_external_paraview-%s.patch' % paraversion, -] +checksums = ['294b520811aae87241f3a78423f05952'] + +patches = ['OpenFOAM-%(version)s-cleanup.patch'] dependencies = [ - ('CGAL', '4.8.1'), ('libreadline', '6.3'), - # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) - ('METIS', '5.1.0', '-32bitIDX'), ('ncurses', '6.0'), - ('ParaView', paraversion, '-mpi'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), ('SCOTCH', '6.0.4'), + ('CGAL', '4.8.1'), + ('ParaView', '5.1.2', '-mpi'), ] builddependencies = [ ('Bison', '3.0.4'), - ('CMake', '3.5.2'), + ('CMake', '3.6.1'), ('flex', '2.6.0'), ] -- GitLab From 782ce32318fdba927d7c17a9278fc3db115bd745 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 5 Sep 2016 13:20:56 +0200 Subject: [PATCH 373/701] Add forgotten METIS patch --- .../m/METIS/METIS-5.1.0-use-doubles.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch new file mode 100644 index 0000000000..206f7ae1ae --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch @@ -0,0 +1,13 @@ +# Use double for floating point (64 bit) in METIS by default +diff -ur metis-5.1.0.orig/include/metis.h metis-5.1.0/include/metis.h +--- metis-5.1.0.orig/include/metis.h 2013-03-30 17:24:45.000000000 +0100 ++++ metis-5.1.0/include/metis.h 2016-09-05 11:39:33.004384533 +0200 +@@ -40,7 +40,7 @@ + 32 : single precission floating point (float) + 64 : double precission floating point (double) + --------------------------------------------------------------------------*/ +-#define REALTYPEWIDTH 32 ++#define REALTYPEWIDTH 64 + + + -- GitLab From d96a1d9fcc68f5fe3236043d1f1fe1da1d2a9ebe Mon Sep 17 00:00:00 2001 From: Appmaint Date: Mon, 5 Sep 2016 13:12:27 +0100 Subject: [PATCH 374/701] FFTW 3.3.5 with gompi 2016.07 toolchain --- .../f/FFTW/FFTW-3.3.5-gompi-2016.07.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb new file mode 100644 index 0000000000..2696fc3313 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +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': '2016.07'} +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 f3c411dc857a8e3a8a62bbb86c51f30e0baaf12a Mon Sep 17 00:00:00 2001 From: Appmaint Date: Mon, 5 Sep 2016 13:16:11 +0100 Subject: [PATCH 375/701] Remove optarch statement in toolchainopts --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb index 2696fc3313..854d665922 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.07.eb @@ -8,7 +8,7 @@ description = """FFTW is a C subroutine library for computing the discrete Fouri in one or more dimensions, of arbitrary input size, and of both real and complex data.""" toolchain = {'name': 'gompi', 'version': '2016.07'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -- GitLab From 64aa662e8bd3d92f9176c41c189445fa9d667b98 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 5 Sep 2016 15:44:30 +0200 Subject: [PATCH 376/701] Remove rotortest from testlist --- .../OpenBabel-2.3.2-comparison.patch | 58 ------------------- ...penBabel-2.3.2-foss-2016a-Python-2.7.11.eb | 2 +- .../OpenBabel-2.3.2-ignore-rotor-test.patch | 12 ++++ 3 files changed, 13 insertions(+), 59 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-comparison.patch create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ignore-rotor-test.patch diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-comparison.patch b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-comparison.patch deleted file mode 100644 index 07b07de115..0000000000 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-comparison.patch +++ /dev/null @@ -1,58 +0,0 @@ -# From: https://sourceforge.net/p/openbabel/bugs/945/ -# Rotor tests fail on ppc architecture, because the checks for the expected value don't take into account the modulus. This patch should fix the issue. -# Author: Susi Lehtola -diff -up openbabel-2.3.2/include/openbabel/obutil.h.orig openbabel-2.3.2/include/openbabel/obutil.h ---- openbabel-2.3.2/include/openbabel/obutil.h.orig 2010-10-09 19:05:12.000000000 -0700 -+++ openbabel-2.3.2/include/openbabel/obutil.h 2014-10-16 16:35:49.050074389 -0700 -@@ -190,6 +190,8 @@ namespace OpenBabel - * \deprecated Use IsApprox() instead - */ - OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); -+ //! Same but with comparison with a modulus -+ OBAPI bool IsNear_mod(const double &, const double &, const double & mod, const double epsilon=2e-6); - /*! "Safe" comparison for floats/doubles: true if a is less than epsilon - * This function really doesn't make any sense w.r.t. floating-point - * representation, so you should never use it. It is provided only for -diff -up openbabel-2.3.2/src/obutil.cpp.orig openbabel-2.3.2/src/obutil.cpp ---- openbabel-2.3.2/src/obutil.cpp.orig 2012-10-03 12:08:15.000000000 -0700 -+++ openbabel-2.3.2/src/obutil.cpp 2014-10-16 16:54:18.309740019 -0700 -@@ -77,6 +77,18 @@ namespace OpenBabel - return (fabs(a - b) < epsilon); - } - -+ //! Comparison for doubles with a modulus: returns mod(a - b,m) < epsilon -+ bool IsNear_mod(const double &a, const double &b, const double &m, const double epsilon) -+ { -+ double arg=a-b; -+ while(arg<-m/2) -+ arg+=m; -+ while(arg>=m/2) -+ arg-=m; -+ -+ return (fabs(arg) < epsilon); -+ } -+ - //! Comparison for doubles: returns fabs(a) < epsilon - bool IsNearZero(const double &a, const double epsilon) - { -diff -up openbabel-2.3.2/test/rotortest.cpp.orig openbabel-2.3.2/test/rotortest.cpp ---- openbabel-2.3.2/test/rotortest.cpp.orig 2011-10-12 13:24:02.000000000 -0700 -+++ openbabel-2.3.2/test/rotortest.cpp 2014-10-16 16:54:32.869985348 -0700 -@@ -74,7 +74,7 @@ void testOBRotorSetToAngle() - atoms[i] = (atoms[i] - 1) * 3; - rotor.SetRotAtoms(atoms); - -- OB_ASSERT(IsNear(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 1.0)); -+ OB_ASSERT(IsNear_mod(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 360.0, 1.0)); - - // rotate - rotor.SetToAngle(mol->GetCoordinates(), 60.0 * DEG_TO_RAD); -@@ -106,7 +106,7 @@ void testOBRotorSetRotor() - atoms[i] = (atoms[i] - 1) * 3; - rotor.SetRotAtoms(atoms); - -- OB_ASSERT(IsNear(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 1.0)); -+ OB_ASSERT(IsNear_mod(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 360.0, 1.0)); - rotor.SetToAngle(mol->GetCoordinates(), 60.0 * DEG_TO_RAD); - - // set torsion values diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb index 8d4c77f654..ce69b4afde 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-foss-2016a-Python-2.7.11.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenBabel-%(version)s-fix-link-path-tests.patch', 'OpenBabel-%(version)s-ignore-failed-test.patch', - 'OpenBabel-%(version)s-comparison.patch', + 'OpenBabel-%(version)s-ignore-rotor-test.patch', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ignore-rotor-test.patch b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ignore-rotor-test.patch new file mode 100644 index 0000000000..8783154988 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ignore-rotor-test.patch @@ -0,0 +1,12 @@ +# The rotor tests fails, it is removed from the test set. +# Author: Ruben van Dijk (University of Groningen) +--- test/CMakeLists.txt.orig 2016-09-05 15:17:23.000000000 +0200 ++++ test/CMakeLists.txt 2016-09-05 15:17:38.000000000 +0200 +@@ -18,7 +18,6 @@ + implicitH + lssr + isomorphism +- rotor + shuffle + smiles + spectrophore -- GitLab From d20f3c7505b38798ffb1c0ab78b413481db6f4b4 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Mon, 5 Sep 2016 15:33:32 +0100 Subject: [PATCH 377/701] Python 3.5.2 with toolchain foss 2016.04 + deps --- .../a/Autoconf/Autoconf-2.69-foss-2016.04.eb | 26 ++++ .../a/Automake/Automake-1.15-foss-2016.04.eb | 33 +++++ .../Autotools-20150215-foss-2016.04.eb | 17 +++ .../b/bzip2/bzip2-1.0.6-foss-2016.04.eb | 16 +++ .../g/GMP/GMP-6.1.1-foss-2016.04.eb | 30 +++++ .../g/gettext/gettext-0.19.8-foss-2016.04.eb | 23 ++++ .../l/libffi/libffi-3.2.1-foss-2016.04.eb | 23 ++++ .../libreadline-6.3-foss-2016.04.eb | 32 +++++ .../l/libtool/libtool-2.4.6-foss-2016.04.eb | 17 +++ .../l/libxml2/libxml2-2.9.4-foss-2016.04.eb | 29 +++++ .../m/M4/M4-1.4.17-foss-2016.04.eb | 23 ++++ .../o/OpenSSL/OpenSSL-1.0.2h-foss-2016.04.eb | 19 +++ .../p/Python/Python-3.5.2-foss-2016.04.eb | 117 ++++++++++++++++++ .../s/SQLite/SQLite-3.13.0-foss-2016.04.eb | 40 ++++++ .../t/Tcl/Tcl-8.6.5-foss-2016.04.eb | 25 ++++ .../easyconfigs/t/Tk/Tk-8.6.5-foss-2016.04.eb | 26 ++++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb | 30 +++++ .../z/zlib/zlib-1.2.8-foss-2016.04.eb | 22 ++++ 18 files changed, 548 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016.04.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016.04.eb new file mode 100644 index 0000000000..94bbfc01ec --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016.04.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': 'foss', 'version': '2016.04'} + +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-foss-2016.04.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb new file mode 100644 index 0000000000..40213b047b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.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': 'foss', 'version': '2016.04'} + +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-foss-2016.04.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016.04.eb new file mode 100644 index 0000000000..05ba2a5c75 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016.04.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': 'foss', 'version': '2016.04'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb new file mode 100644 index 0000000000..deec24c55d --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb @@ -0,0 +1,16 @@ +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': '2016.04'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016.04.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016.04.eb new file mode 100644 index 0000000000..81653e7d61 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016.04.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.1' + +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': 'foss', 'version': '2016.04'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb new file mode 100644 index 0000000000..47b250264e --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8' + +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': '2016.04'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.4'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016.04.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016.04.eb new file mode 100644 index 0000000000..37b990fbd3 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016.04.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': '2016.04'} + +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' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016.04.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016.04.eb new file mode 100644 index 0000000000..14fbd4b55e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016.04.eb @@ -0,0 +1,32 @@ +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': '2016.04'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +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/libtool/libtool-2.4.6-foss-2016.04.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016.04.eb new file mode 100644 index 0000000000..bc63db0c69 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016.04.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': 'foss', 'version': '2016.04'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb new file mode 100644 index 0000000000..32944c28ac --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.4' + +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': 'foss', 'version': '2016.04'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb new file mode 100644 index 0000000000..ef1614fe9a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.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': '2016.04'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-foss-2016.04.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-foss-2016.04.eb new file mode 100644 index 0000000000..71a267bdce --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-foss-2016.04.eb @@ -0,0 +1,19 @@ +name = 'OpenSSL' +version = '1.0.2h' + +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': '2016.04'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb new file mode 100644 index 0000000000..89d653c10d --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb @@ -0,0 +1,117 @@ +name = 'Python' +version = '3.5.2' + +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': '2016.04'} +toolchainopts = {'pic': 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', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + ('GMP', '6.1.1'), + ('XZ', '5.2.2'), + ('libffi', '3.2.1'), + # 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', '1.0.2h'), +] + +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '23.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('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/'], + }), + ('pbr', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.24', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.5.3', { + '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', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + '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/'], + }), + ('cryptography', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.1.5', { + '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', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('pandas', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('virtualenv', '15.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.eb new file mode 100644 index 0000000000..ee0989cdf4 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.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 = '3.13.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2016.04'} + +source_urls = ['http://www.sqlite.org/2016/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.5'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016.04.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016.04.eb new file mode 100644 index 0000000000..c3516cdb44 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016.04.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.5' + +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': '2016.04'} + +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-8.6.5-foss-2016.04.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016.04.eb new file mode 100644 index 0000000000..5587e8e8dc --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016.04.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +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': '2016.04'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb new file mode 100644 index 0000000000..0faab98c7c --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'foss', 'version': '2016.04'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('gettext', '0.19.8'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb new file mode 100644 index 0000000000..042a9bef50 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.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': 'foss', 'version': '2016.04'} +toolchainopts = {'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 b9af80f1e16141231d5d2f8cbe628ea6aad6677b Mon Sep 17 00:00:00 2001 From: Appmaint Date: Mon, 5 Sep 2016 15:41:58 +0100 Subject: [PATCH 378/701] Comment out OpenSSL --- easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb index 89d653c10d..2581a2015d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb @@ -24,10 +24,10 @@ dependencies = [ ('libffi', '3.2.1'), # 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', '1.0.2h'), + #('OpenSSL', '1.0.2h'), ] -#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 -- GitLab From 664907be3506c1a5a0de279207606ca56f883131 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Mon, 5 Sep 2016 16:20:39 +0100 Subject: [PATCH 379/701] foss 2016.09 experimental toolchain --- .../f/FFTW/FFTW-3.3.5-gompi-2016.09.eb | 34 +++++++++++++ easybuild/easyconfigs/f/foss/foss-2016.09.eb | 35 +++++++++++++ .../easyconfigs/g/gompi/gompi-2016.09.eb | 20 ++++++++ .../easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb | 18 +++++++ .../h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb | 23 +++++++++ .../numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb | 23 +++++++++ ...nBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb | 49 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb | 42 ++++++++++++++++ ...pi-2016.09-OpenBLAS-0.2.19-LAPACK-3.6.1.eb | 25 ++++++++++ 9 files changed, 269 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2016.09.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2016.09.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.09-OpenBLAS-0.2.19-LAPACK-3.6.1.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb new file mode 100644 index 0000000000..624cde1f79 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +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': '2016.09'} +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-2016.09.eb b/easybuild/easyconfigs/f/foss/foss-2016.09.eb new file mode 100644 index 0000000000..89b1d45732 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.09.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.09' + +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 = '6.2.0-2.27' + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.1' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# 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), + ('OpenMPI', '2.0.1', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, comp_mpi_tc), + ('FFTW', '3.3.5', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc) +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb new file mode 100644 index 0000000000..b4350de73a --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.09' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, +including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.2.0-2.27' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC and binutils + ('OpenMPI', '2.0.1', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb new file mode 100644 index 0000000000..4237ac091d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +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': '2016.09'} +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-1.11.4-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb new file mode 100644 index 0000000000..35ced3699b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.4' + +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': 'GCC', 'version': '6.2.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb new file mode 100644 index 0000000000..7d6ccf3999 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +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': 'GCC', 'version': '6.2.0-2.27'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb new file mode 100644 index 0000000000..32b66ddad1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.19' + +lapackver = '3.6.1' +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': '2016.09'} + +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="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb new file mode 100644 index 0000000000..ee1f9a9554 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.1' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} + +sources = [SOURCELOWER_TAR_GZ] + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] + +dependencies = [('hwloc', '1.11.4')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-tm=/usr/local/packages/adaptive/torque ' # we want torque support as well + +# Add in support for hardware from Mellanox OFED +configopts += '--with-mxm=/opt/mellanox/mxm ' +configopts += '--with-fca=/opt/mellanox/fca ' +#configopts += '--with-hcoll=/opt/mellanox/hcoll ' +configopts += '--with-knem=/opt/knem-1.1.2.90mlnx1 ' # knem comes from Mellanox OFED +configopts += '--with-platform=contrib/platform/mellanox/optimized ' + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'), ('libpciaccess-devel'), ('libudev-devel', 'systemd-devel'),] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "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] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/c"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.09-OpenBLAS-0.2.19-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.09-OpenBLAS-0.2.19-LAPACK-3.6.1.eb new file mode 100644 index 0000000000..8fcb8f6610 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.09-OpenBLAS-0.2.19-LAPACK-3.6.1.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': '2016.09'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.6.1' + +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 43fba03218f09cbb324ce2733bf1efaa0e837a1e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 6 Sep 2016 09:41:38 +0200 Subject: [PATCH 380/701] Bump Mesa to 12.0.2 --- .../{Mesa-12.0.1-intel-2016b.eb => Mesa-12.0.2-intel-2016b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/Mesa/{Mesa-12.0.1-intel-2016b.eb => Mesa-12.0.2-intel-2016b.eb} (99%) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb similarity index 99% rename from easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb rename to easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index 821ca3a0b7..52daa51051 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -8,7 +8,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' -version = '12.0.1' +version = '12.0.2' homepage = 'http://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - -- GitLab From 395fed43239f30aabbb67a6900d23931b38d992c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 6 Sep 2016 09:44:56 +0200 Subject: [PATCH 381/701] Bump libGLU to new mesa too --- easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb index 1bfa6744b9..51bb338e1e 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb @@ -13,7 +13,7 @@ source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] sources = ['glu-%(version)s.tar.bz2'] dependencies = [ - ('Mesa', '12.0.1'), + ('Mesa', '12.0.2'), ] sanity_check_paths = { -- GitLab From 49a2f04d727d8d5277c70474964b794ac2434e74 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 6 Sep 2016 09:47:14 +0200 Subject: [PATCH 382/701] Bump to Mesa/12.0.2 --- easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb | 2 +- .../easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb index 1bfa6744b9..51bb338e1e 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2016b.eb @@ -13,7 +13,7 @@ source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] sources = ['glu-%(version)s.tar.bz2'] dependencies = [ - ('Mesa', '12.0.1'), + ('Mesa', '12.0.2'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb index 1b7e04902f..351d316159 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb @@ -16,7 +16,7 @@ sources = ["ParaView-v%(version)s.tar.gz"] dependencies = [ ('X11', '20160819'), - ('Mesa', '12.0.1'), + ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), ('Qt', '4.8.7'), ('zlib', '1.2.8'), -- GitLab From 6385ff59c6e5ce8ed6423d53bf48dc5cf06b749c Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 6 Sep 2016 09:55:14 +0200 Subject: [PATCH 383/701] Removed GCCcore subtoolchain from Autotools dependency, as using --minimal-toolchains will use subtoolchains automatically. --- easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb index 6dd4849514..b4e90a24ee 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.5-foss-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] -builddependencies = [('Autotools', '20150215', '', ('GCCcore', '4.9.3'))] +builddependencies = [('Autotools', '20150215')] dependencies = [('libunwind', '1.1')] sanity_check_paths = { -- GitLab From fef877d53be783cf0d7683116d9cf82dd0b38fbf Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 6 Sep 2016 10:04:58 +0200 Subject: [PATCH 384/701] Fix remarks --- .../easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch | 1 + .../p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb | 10 ++++++---- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch index 206f7ae1ae..f02824071e 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-use-doubles.patch @@ -1,4 +1,5 @@ # Use double for floating point (64 bit) in METIS by default +# OpenFOAM 4 uses doubles be default diff -ur metis-5.1.0.orig/include/metis.h metis-5.1.0/include/metis.h --- metis-5.1.0.orig/include/metis.h 2013-03-30 17:24:45.000000000 +0100 +++ metis-5.1.0/include/metis.h 2016-09-05 11:39:33.004384533 +0200 diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb index 351d316159..59f802689e 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.1.2-intel-2016b-mpi.eb @@ -29,13 +29,15 @@ builddependencies = [('CMake', '3.6.1')] separate_build_dir = True configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' -configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' -configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' -configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.so ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + # Without internet connection turn off testing (uncomment the following line) configopts += '-DBUILD_TESTING=OFF ' -#configopts += '-DVTK_USE_X=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) -- GitLab From d0b90114b4bcb1642f045b95066aec3123f0cfad Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 6 Sep 2016 10:23:47 +0200 Subject: [PATCH 385/701] Don't use oparch in Mesa It builds a part that only works for AVX or AVX2, so don't force -xHost on it (it will cause failures). --- easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index 52daa51051..dd4fd96df3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -15,6 +15,7 @@ description = """Mesa is an open-source implementation of the OpenGL specificati a system for rendering interactive 3D graphics.""" toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'optarch': False} sources = [SOURCELOWER_TAR_XZ] source_urls = [ -- GitLab From 8dcac2a9dc40b4bd7bd7bfb646ce94f2c691da69 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 6 Sep 2016 10:54:01 +0200 Subject: [PATCH 386/701] Add comment --- easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index dd4fd96df3..90fd4b0810 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -15,6 +15,8 @@ description = """Mesa is an open-source implementation of the OpenGL specificati a system for rendering interactive 3D graphics.""" toolchain = {'name': 'intel', 'version': '2016b'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. toolchainopts = {'optarch': False} sources = [SOURCELOWER_TAR_XZ] -- GitLab From 4397e35f4d220d669b08196ac8203b28dcf37a9c Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 6 Sep 2016 10:06:17 +0100 Subject: [PATCH 387/701] Removed site-specifics and dropped optarch --- .../easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb | 2 +- .../o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb | 11 +---------- 2 files changed, 2 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb index 624cde1f79..95601b61f5 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016.09.eb @@ -8,7 +8,7 @@ description = """FFTW is a C subroutine library for computing the discrete Fouri in one or more dimensions, of arbitrary input size, and of both real and complex data.""" toolchain = {'name': 'gompi', 'version': '2016.09'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb index ee1f9a9554..67deb43507 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -18,20 +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 += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-tm=/usr/local/packages/adaptive/torque ' # we want torque support as well - -# Add in support for hardware from Mellanox OFED -configopts += '--with-mxm=/opt/mellanox/mxm ' -configopts += '--with-fca=/opt/mellanox/fca ' -#configopts += '--with-hcoll=/opt/mellanox/hcoll ' -configopts += '--with-knem=/opt/knem-1.1.2.90mlnx1 ' # knem comes from Mellanox OFED -configopts += '--with-platform=contrib/platform/mellanox/optimized ' # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'), ('libpciaccess-devel'), ('libudev-devel', 'systemd-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] libs = ["mpi_mpifh", "mpi", "ompitrace", "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 e86657a175b7d40e8a90cf19b7e578c342c8c84d Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 6 Sep 2016 10:12:05 +0100 Subject: [PATCH 388/701] Dropped optarch in HPL --- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb index 4237ac091d..be4db4593e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb @@ -7,7 +7,7 @@ description = """HPL is a software package that solves a (random) dense linear s High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.09'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] -- GitLab From a5af53150f793b37c26a66fdb5e2093711c43e40 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 6 Sep 2016 10:21:40 +0100 Subject: [PATCH 389/701] Made requested changes --- .../easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb | 9 --------- easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb | 2 +- 2 files changed, 1 insertion(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb index 32944c28ac..645a9c0d23 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.4' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb index 042a9bef50..a484ded000 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016.04.eb @@ -15,7 +15,7 @@ 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'], + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From 8d370dd66c539610d436ff881362dcb50f855ee1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 11:24:13 +0200 Subject: [PATCH 390/701] bump IronPython to 2.7.4 --- ...4.1.13-g4fb2552.eb => IronPython-2.7.4-ictce-4.1.13.eb} | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/i/IronPython/{IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb => IronPython-2.7.4-ictce-4.1.13.eb} (71%) diff --git a/easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb b/easybuild/easyconfigs/i/IronPython/IronPython-2.7.4-ictce-4.1.13.eb similarity index 71% rename from easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb rename to easybuild/easyconfigs/i/IronPython/IronPython-2.7.4-ictce-4.1.13.eb index fb3ff7bded..7b6a5a5013 100644 --- a/easybuild/easyconfigs/i/IronPython/IronPython-2.7-0-ictce-4.1.13-g4fb2552.eb +++ b/easybuild/easyconfigs/i/IronPython/IronPython-2.7.4-ictce-4.1.13.eb @@ -1,6 +1,5 @@ name = 'IronPython' -version = '2.7-0' -versionsuffix = '-g4fb2552' +version = '2.7.4' homepage = 'http://ironpython.net/' description = """IronPython is an open-source implementation of the Python programming language @@ -9,8 +8,8 @@ Python libraries, and other .NET languages can use Python code just as easily."" toolchain = {'name': 'ictce', 'version': '4.1.13'} -# download via https://github.com/IronLanguages/main/releases -sources = ['IronLanguages-main-ipy-%(version)s%(versionsuffix)s.tar.gz'] +source_urls = ['https://github.com/IronLanguages/main/archive/'] +sources = ['ipy-%(version)s.tar.gz'] dependencies = [('Mono', '2.10.6')] -- GitLab From 2bed2ec6925c5d98bd08c1789070e23724eb5cc5 Mon Sep 17 00:00:00 2001 From: Appmaint Date: Tue, 6 Sep 2016 10:27:40 +0100 Subject: [PATCH 391/701] Fixed sanity check --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb index 67deb43507..aeb2a52e4c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -27,7 +27,7 @@ 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] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/c"], + 'dirs': [], } moduleclass = 'mpi' -- GitLab From dcda585c1c6b4ce34e11e2bbe55faa2e5a5854b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 11:35:11 +0200 Subject: [PATCH 392/701] stick to IronPython 2.7, since that works --- ...n-2.7.4-ictce-4.1.13.eb => IronPython-2.7-ictce-4.1.13.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/IronPython/{IronPython-2.7.4-ictce-4.1.13.eb => IronPython-2.7-ictce-4.1.13.eb} (90%) diff --git a/easybuild/easyconfigs/i/IronPython/IronPython-2.7.4-ictce-4.1.13.eb b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-ictce-4.1.13.eb similarity index 90% rename from easybuild/easyconfigs/i/IronPython/IronPython-2.7.4-ictce-4.1.13.eb rename to easybuild/easyconfigs/i/IronPython/IronPython-2.7-ictce-4.1.13.eb index 7b6a5a5013..147957947e 100644 --- a/easybuild/easyconfigs/i/IronPython/IronPython-2.7.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-ictce-4.1.13.eb @@ -1,7 +1,7 @@ name = 'IronPython' -version = '2.7.4' +version = '2.7' -homepage = 'http://ironpython.net/' +homepage = 'http://ironpython.net/' description = """IronPython is an open-source implementation of the Python programming language which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and Python libraries, and other .NET languages can use Python code just as easily.""" -- GitLab From 09a09e45c73a793776d365b6d7aecb5682ebcc01 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 6 Sep 2016 11:52:46 +0200 Subject: [PATCH 393/701] Fix Qt5 for RHEL 6.x --- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb index 0710553732..589ca4e25a 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016b.eb @@ -20,6 +20,9 @@ builddependencies = [ ('pkg-config', '0.29.1'), ] +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + dependencies = [ ('GLib', '2.49.5'), ('libpng', '1.6.24'), -- GitLab From 9699daf62ce5ab197d76314fb5ada18870212f83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 12:32:13 +0200 Subject: [PATCH 394/701] bump to Bison 2.7, don't force parallel=1 in Mono easyconfig --- easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb index 05e81f5396..2971b15c53 100644 --- a/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-ictce-4.1.13.eb @@ -21,10 +21,8 @@ sources = [ ] builddependencies = [ - ('Bison', '2.6.5'), + ('Bison', '2.7'), ('gettext', '0.18.2'), ] -parallel = 1 - moduleclass = 'lang' -- GitLab From ad963b925ffe5f1a59d35e266acf8a66ffc56f9d Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 6 Sep 2016 12:46:49 +0200 Subject: [PATCH 395/701] Version of ATK built using the foss 2016a toolchain. --- .../a/ATK/ATK-2.20.0-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb new file mode 100644 index 0000000000..0f7c93a41d --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.20.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +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': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 57fb2ba7ef129879def2e7e16acaeba677d8c6de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 12:59:02 +0200 Subject: [PATCH 396/701] disable qtgamepad in Qt5 easyconfig --- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb index 82e71ce75d..a387649d5b 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb @@ -50,4 +50,7 @@ dependencies = [ ('libGLU', '9.0.0', '-Mesa-11.2.1'), ] +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + moduleclass = 'devel' -- GitLab From c9a428c70cb3923aad04982890712d89fc490959 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 13:00:48 +0200 Subject: [PATCH 397/701] disable qtgamepad in Qt5 easyconfig --- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb index 50c78a140e..1ccc867425 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb @@ -50,4 +50,7 @@ dependencies = [ ('libGLU', '9.0.0', '-Mesa-11.2.1'), ] -moduleclass = 'devel' \ No newline at end of file +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +moduleclass = 'devel' -- GitLab From c6ccbcc81a5048e7eafe6833746af2e6f3eacd17 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 13:24:59 +0200 Subject: [PATCH 398/701] remove irrelevant comment in log4cplus easyconfigs --- .../easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb | 1 - easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb index e88e8c2f72..9606b8555d 100755 --- a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb @@ -10,7 +10,6 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -# make sure the gzip, gunzip and compress binaries are available after installation sanity_check_paths = { 'files': ["lib/liblog4cplus.a", "lib/liblog4cplus.so"], 'dirs': ["include/log4cplus"], diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb index f5511eacf6..ddd6f60ebf 100755 --- a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb @@ -10,7 +10,6 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -# make sure the gzip, gunzip and compress binaries are available after installation sanity_check_paths = { 'files': ["lib/liblog4cplus.a", "lib/liblog4cplus.so"], 'dirs': ["include/log4cplus"], -- GitLab From ba419506c0aae956a71fc48a263263889f376903 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 13:26:11 +0200 Subject: [PATCH 399/701] add missing easyblock spec --- .../easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb | 2 ++ .../easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb index 9606b8555d..af8ebb2524 100755 --- a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.0.4.3-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'log4cplus' version = '1.0.4.3' diff --git a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb index ddd6f60ebf..bdb9d13739 100755 --- a/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/log4cplus/log4cplus-1.1.2-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'log4cplus' version = '1.1.2' -- GitLab From 6246c832300e1b0705eb73209f19e097ba54f6c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 13:27:00 +0200 Subject: [PATCH 400/701] add missing easyblock spec, use buildopts --- .../easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb index 3218a6e11d..e96e5e3b33 100755 --- a/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FFindex/FFindex-0.9.9-goolf-1.4.10.eb @@ -1,5 +1,7 @@ -name = "FFindex" -version = "0.9.9" +easyblock = 'ConfigureMake' + +name = 'FFindex' +version = '0.9.9' homepage = 'http://www.splashground.de/~andy/programs/FFindex/' description = """simple index/database for huge amounts of small files""" @@ -14,7 +16,7 @@ skipsteps = ['configure'] start_dir = 'src' -makeopts = 'USEMPI=1' +buildopts = 'USEMPI=1' installopts = "USEMPI=1 INSTALL_DIR=%(installdir)s" runtest = 'test' -- GitLab From f64ecba251ed22feb4c780f846c0747a6b4465ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 13:38:32 +0200 Subject: [PATCH 401/701] sync texinfo easyconfig with existing one, add missing easyblock spec in RDMC easyconfig --- .../r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb | 2 ++ .../t/texinfo/texinfo-5.2-ictce-5.5.0.eb | 29 ++++++++++++++----- 2 files changed, 23 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb b/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb index b6cf4c64fb..a768f518ac 100755 --- a/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/RDMC/RDMC-2.9.5-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'RDMC' version = '2.9.5' diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb index dc542d4583..0eff73d3cc 100755 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-ictce-5.5.0.eb @@ -1,18 +1,31 @@ +easyblock = 'ConfigureMake' + name = 'texinfo' version = '5.2' -homepage = 'http://www.gnu.org/software/texinfo/' -description = "Texinfo is the official documentation format of the GNU project." +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://ftpmirror.gnu.org/texinfo'] -sources = [SOURCE_TAR_GZ] +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable \\$TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new \\$TEXMFHOME to your custom directory and reset the value of \\$TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['info', 'infokey', 'install-info', 'makeinfo', 'pdftexi2dvi', 'pod2texi', - 'texi2any', 'texi2dvi', 'texi2pdf', 'texindex']], - 'dirs': ["bin", "share"], + 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf', 'texmf/tex/texinfo/texinfo.tex'], + 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'devel' -- GitLab From a276557da5deb596662d279d954db50516644871 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 13:40:28 +0200 Subject: [PATCH 402/701] Bundle instead of PythonPackage --- .../gensim-0.12.4-foss-2016a-Python-2.7.11.eb | 20 --------- .../gensim-0.13.2-foss-2016a-Python-2.7.11.eb | 43 +++++++++++++++++++ 2 files changed, 43 insertions(+), 20 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index 4c0e09b879..0000000000 --- a/easybuild/easyconfigs/g/gensim/gensim-0.12.4-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'gensim' -version = '0.12.4' -versionsuffix = '-Python-%(pyver)s' - -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': 'foss', 'version': '2016a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.11'), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..6579381696 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,43 @@ +easyblock = 'Bundle' + +name = 'gensim' +version = '0.13.2' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('requests', '2.10.0', '-Python-%(pyver)s'), +] + + +exts_list = [ + ('boto', '2.42.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s'], + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + }), + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s'], + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + }), + ('smart_open', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/s/%(name)s'], + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'lib' \ No newline at end of file -- GitLab From 336f309773b78f218a64f3534d1ff743d2ac7ea7 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 13:48:01 +0200 Subject: [PATCH 403/701] Pyro4 with foss2016a --- .../Pyro4-4.47-foss-2016a-Python-2.7.11.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..53c6523f10 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'Pyro4' +version = '4.47' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/Pyro4' +description = """Pyro means PYthon Remote Objects. It is a library that enables you to build applications in which + objects can talk to eachother over the network, with minimal programming effort.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +options = {'modulename': 'Pyro4'} + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'lib' -- GitLab From c229d62148b487e85d8a572af21663e55b448c5a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 13:55:32 +0200 Subject: [PATCH 404/701] add missing easyblock spec in CFITSIO easyconfig --- .../easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb index e2fd327b03..8c90ec640b 100755 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'CFITSIO' version = '3.300' @@ -6,15 +8,15 @@ description = """CFITSIO is a library of C and Fortran subroutines for reading a FITS (Flexible Image Transport System) data format.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} srcversion = version.replace('.', '') source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { - 'files':["lib/libcfitsio.a"], - 'dirs':["include"], + 'files': ['lib/libcfitsio.a'], + 'dirs': ['include'], } moduleclass = 'lib' -- GitLab From d7771d44143b3ad368abc658444514bfcc834dd0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 14:11:17 +0200 Subject: [PATCH 405/701] Include sanity checks --- easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb | 5 +++++ easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb | 5 +++++ 2 files changed, 10 insertions(+) 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 2f00cc2dbd..013f802b61 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 @@ -21,4 +21,9 @@ sources = [SOURCELOWER_ZIP] dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb index 9fb67afb2a..05e18b2e8b 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb @@ -21,4 +21,9 @@ sources = [SOURCELOWER_ZIP] dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + moduleclass = 'lib' -- GitLab From 24043da125f260ec0d18d5ea8563c03c785991e8 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 14:18:05 +0200 Subject: [PATCH 406/701] change to gensim source --- .../g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb index 6579381696..7022e306a3 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb @@ -33,11 +33,8 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s.tar.gz', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'source_urls': ['https://pypi.python.org/packages/source/g/%(name)s'], }), ] -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - moduleclass = 'lib' \ No newline at end of file -- GitLab From f227e803f1d37f1ce3a558d0b2800398cbd6471e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 14:25:34 +0200 Subject: [PATCH 407/701] sanity checks and modextrapath --- .../gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb index 7022e306a3..991e6da6fa 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb @@ -18,7 +18,6 @@ dependencies = [ ('requests', '2.10.0', '-Python-%(pyver)s'), ] - exts_list = [ ('boto', '2.42.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s'], @@ -37,4 +36,14 @@ exts_list = [ }), ] +# 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': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + moduleclass = 'lib' \ No newline at end of file -- GitLab From 1f3ab1eff2857cc51a0f5aef998489d7f76e6a5f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 14:28:19 +0200 Subject: [PATCH 408/701] Sanity checks --- .../p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb index 53c6523f10..0a1e3fec18 100644 --- a/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pyro4/Pyro4-4.47-foss-2016a-Python-2.7.11.eb @@ -19,4 +19,9 @@ dependencies = [ ('Python', '2.7.11'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + moduleclass = 'lib' -- GitLab From b59b0c10967f0ff171b77a902523b9608bf4d2cd Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 6 Sep 2016 14:44:31 +0200 Subject: [PATCH 409/701] libjpeg-turbo 1.4.2 compiled with the foss 2016a toolchain. This version depends on NASM 2.12.01 and is in line with the intel 2016a version. --- ...peg-turbo-1.4.2-foss-2016a-NASM-2.12.01.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a-NASM-2.12.01.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a-NASM-2.12.01.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a-NASM-2.12.01.eb new file mode 100644 index 0000000000..8728627d19 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016a-NASM-2.12.01.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.2' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +nasmver = '2.12.01' +versionsuffix = '-NASM-%s' % nasmver + +dependencies = [ + ('NASM', nasmver), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' -- GitLab From 129a45002d8a43d8eb6485eb75c2692cd10064ff Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 15:31:22 +0200 Subject: [PATCH 410/701] SHORE with foss2016a --- .../s/SHORE/SHORE-0.9.3-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb new file mode 100644 index 0000000000..c79e6232d8 --- /dev/null +++ b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'SHORE' +version = '0.9.3' + +homepage = "http://1001genomes.org/software/shore.html" +description = """SHORE, for Short Read, is a mapping and analysis pipeline for short read data produced on the Illumina platform. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://sourceforge.net/projects/shore/files/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '--with-mpi' + +dependencies = [ + ('XZ','5.2.2'), + ('zlib','1.2.8'), + ('GSL','1.16'), # GSL 2.1 does not work. +] + +osdependencies = ['boost-devel', 'boost-iostreams', 'boost-thread'] + +sanity_check_paths = { + 'files': ['bin/shore', 'bin/shore-mpi', 'lib/libshore.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'bio' -- GitLab From 36ff147e0b54b690ae6cb37bac9b3f5fad08048c Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 6 Sep 2016 15:56:42 +0200 Subject: [PATCH 411/701] Gdk-Pixbuf using the foss 2016a toolchain. --- .../Gdk-Pixbuf-2.35.1-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb new file mode 100644 index 0000000000..3f2a2533d6 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.35.1-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.35.1' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From 4874963c0fa5c81680a767cd9e1e0404d0c4add4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 16:12:13 +0200 Subject: [PATCH 412/701] PyQt5 with foss2016a --- .../PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ .../SIP-4.18.1-foss-2016a-Python-2.7.11.eb | 30 ++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..ea548f357c --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt5' +version = '5.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(name)s_gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-%(version)s'] + +dependencies = [ + ('Python', '2.7.11'), + ('SIP', '4.18.1', versionsuffix), + ('Qt5', '5.7.0'), +] + +configopts = "configure.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], +} + +moduleclass = 'vis' \ No newline at end of file diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..dbc48b8044 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +# 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 = '4.18.1' +versionsuffix = '-Python-%(pyver)s' + +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': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.11')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 537bbfaa8972fff17f09a1c43640b47594ed5b85 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 16:14:34 +0200 Subject: [PATCH 413/701] Fix sanity check --- .../p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb index ea548f357c..6cc9d5dd83 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb @@ -28,7 +28,7 @@ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], } -moduleclass = 'vis' \ No newline at end of file +moduleclass = 'vis' -- GitLab From bc996ae478603e1e8eeb15c15e35aee76dec150a Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 16:15:30 +0200 Subject: [PATCH 414/701] Filename version changed --- ...16a-Python-2.7.11.eb => PyQT5-5.7-foss-2016a-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PyQt5/{PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb => PyQT5-5.7-foss-2016a-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7-foss-2016a-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/p/PyQt5/PyQT5-5.7.0-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/p/PyQt5/PyQT5-5.7-foss-2016a-Python-2.7.11.eb -- GitLab From 91b9458daedc8ad337b717228d216f5754ea5967 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 6 Sep 2016 16:41:02 +0200 Subject: [PATCH 415/701] Version of Harfbuzz using the foss 2016a toolchain. The config is based on the intel 2016a one. --- .../h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb new file mode 100644 index 0000000000..1c081e2c8e --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.2.7-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.2.7' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('freetype', '2.6.3'), + ('GObject-Introspection', '1.48.0') +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 1c8e0019d4b515d05af44fc73ef6d246148dac1c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 6 Sep 2016 16:08:19 +0100 Subject: [PATCH 416/701] Update deps to NGS-1.2.5 and ncbi-vdb-2.7.0 --- .../h/HISAT2/HISAT2-2.0.4-foss-2016b.eb | 4 +- .../easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb | 35 +++++++++++++++++ .../n/ncbi-vdb/ncbi-vdb-2.7.0-foss-2016b.eb | 38 +++++++++++++++++++ 3 files changed, 75 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.7.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb index 354eb721c4..83a592d05a 100644 --- a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb @@ -15,8 +15,8 @@ source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] checksums = ['50119a693929e240b072d79e69dc211e'] dependencies = [ - ('NGS', '1.2.3'), - ('ncbi-vdb', '2.5.8-1'), + ('NGS', '1.2.5'), + ('ncbi-vdb', '2.7.0'), ] buildopts = "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb new file mode 100644 index 0000000000..8b032e0468 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.2.5' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_92', '', True)] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.7.0-foss-2016b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.7.0-foss-2016b.eb new file mode 100644 index 0000000000..077b870927 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.7.0-foss-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.7.0' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('file', '5.28'), # provides libmagic + ('HDF5', '1.8.17'), + ('NGS', '1.2.5'), +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 48ec2d383a04713baafef1c137d6ba8db12c38de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 18:35:24 +0200 Subject: [PATCH 417/701] add easyconfig VTK-7.0.0-intel-2016b-Python-2.7.12.eb --- .../VTK-7.0.0-intel-2016b-Python-2.7.12.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ce85c69cbd --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,58 @@ +## +# 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_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '7.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.6.1')] + +dependencies = [ + ('Python', '2.7.12'), + ('libGLU', '9.0.0'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', 'mkg3states']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' -- GitLab From 1303b95d7b0958811e8291d78f61a7c844f72afe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 18:37:34 +0200 Subject: [PATCH 418/701] add easyconfig CGAL-4.8.1-intel-2016b-Python-2.7.12.eb --- .../CGAL-4.8.1-intel-2016b-Python-2.7.12.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3efaca57eb --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('Boost', '1.61.0', versionsuffix), + ('MPFR', '3.1.4'), + ('GMP', '6.1.1'), + ('libGLU', '9.0.0'), + ('Qt5', '5.7.0'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Eigen', '3.2.9'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' -- GitLab From 70a4f3d2302e2578b992eb1cc1787e5bc6b7693f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 18:50:54 +0200 Subject: [PATCH 419/701] add easyconfig GL2PS-1.3.9-intel-2016b.eb, add easyconfig freeglut-3.0.0-intel-2016b.eb --- .../f/freeglut/freeglut-3.0.0-intel-2016b.eb | 34 +++++++++++++++++++ .../g/GL2PS/GL2PS-1.3.9-intel-2016b.eb | 32 +++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016b.eb new file mode 100644 index 0000000000..ccad2796aa --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.6.1')] + +dependencies = [ + ('X11', '20160819'), + ('Mesa', '12.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016b.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016b.eb new file mode 100644 index 0000000000..1afefc8e72 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.3.9-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.3.9' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.6.1'), +] + +dependencies = [ + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('freeglut', '3.0.0'), + ('libpng', '1.6.24'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 97c4574fd583f5bb184dc3ca450f453af417a5e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 18:54:30 +0200 Subject: [PATCH 420/701] add easyconfig libQGLViewer-2.6.3-intel-2016b.eb --- .../libQGLViewer-2.6.3-intel-2016b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016b.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016b.eb new file mode 100644 index 0000000000..4edf05a0d2 --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.3-intel-2016b.eb @@ -0,0 +1,20 @@ +name = 'libQGLViewer' +version = '2.6.3' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libGLU', '9.0.0'), +] + +builddependencies = [('Qt', '4.8.7')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' -- GitLab From 0bdf7d6133dda4d5386dc54f7672b66f9137a631 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 20:21:03 +0200 Subject: [PATCH 421/701] Name change --- ...16a-Python-2.7.11.eb => PyQt5-5.7-foss-2016a-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PyQt5/{PyQT5-5.7-foss-2016a-Python-2.7.11.eb => PyQt5-5.7-foss-2016a-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQT5-5.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/p/PyQt5/PyQT5-5.7-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb -- GitLab From f46513e8f9ee61f9b135d862a7546bb7c53100b1 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 6 Sep 2016 20:26:40 +0200 Subject: [PATCH 422/701] Boost not as osdep --- easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb index c79e6232d8..756efd9115 100644 --- a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb @@ -18,10 +18,9 @@ dependencies = [ ('XZ','5.2.2'), ('zlib','1.2.8'), ('GSL','1.16'), # GSL 2.1 does not work. + ('Boost', '1.61.0'), ] -osdependencies = ['boost-devel', 'boost-iostreams', 'boost-thread'] - sanity_check_paths = { 'files': ['bin/shore', 'bin/shore-mpi', 'lib/libshore.a'], 'dirs': ['include', 'lib'], -- GitLab From fff0828d44ae2fbfc432717df2ba0f417d7d0e1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2016 21:02:21 +0200 Subject: [PATCH 423/701] add easyconfig Yade-2016.06a-intel-2016b-Python-2.7.12.eb, add easyconfig VTK-6.3.0-intel-2016b-Python-2.7.12.eb --- .../VTK-6.3.0-intel-2016b-Python-2.7.12.eb | 59 ++++++++++++++++++ ...Yade-2016.06a-intel-2016b-Python-2.7.12.eb | 60 +++++++++++++++++++ 2 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..d63c30f413 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,59 @@ +## +# 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_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '6.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.6.1')] + +dependencies = [ + ('Python', '2.7.12'), + ('libGLU', '9.0.0'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource', + 'mkg3states', 'ParseOGLExt']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a7a4e68aef --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,60 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '2016.06a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Yade-%(version)s_include-signal.patch'] + +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('CGAL', '4.8.1', versionsuffix), + ('Eigen', '3.2.9'), + ('GDB', '7.11.1', versionsuffix), + ('GL2PS', '1.3.9'), + ('GTS', '0.7.6'), + ('IPython', '5.1.0', versionsuffix), + ('libQGLViewer', '2.6.3'), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.2', versionsuffix), + ('minieigen', '0.5.3', versionsuffix), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.12'), + ('Qt5', '5.7.0'), + ('SQLite', '3.13.0'), + ('VTK', '6.3.0', versionsuffix), + ('zlib', '1.2.8'), +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], +} + +sanity_check_paths = { + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', + ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, + 'lib64/yade-%%(version)s/libyade.%s' %SHLIB_EXT)], + 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], +} + +moduleclass = 'devel' -- GitLab From f7bda1ae176921f1b0316b1cc23b34426a0a1bc6 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 7 Sep 2016 09:13:09 +0200 Subject: [PATCH 424/701] Version of Pango compiled using the foss 2016a toolchain. The config is based on the intel 2016a version. --- .../p/Pango/Pango-1.40.1-foss-2016a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb new file mode 100644 index 0000000000..70136d70c1 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.1' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('GLib', glibver), + ('cairo', '1.14.6', '-GLib-%s' % glibver), + ('HarfBuzz', '1.2.7'), + ('GObject-Introspection', '1.48.0'), + ('fontconfig', '2.11.95') +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From b7f123a24333b484a545cd17abc51d12eb46c094 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 7 Sep 2016 10:04:58 +0200 Subject: [PATCH 425/701] Version of GTK+ using the foss 2016a toolchain. The config is based on the intel 2016a version. --- .../g/GTK+/GTK+-2.24.30-foss-2016a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb new file mode 100644 index 0000000000..f8cd4f7bed --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.30' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.20.0'), + ('Gdk-Pixbuf', '2.35.1'), + ('Pango', '1.40.1'), + ('GObject-Introspection', '1.48.0'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' -- GitLab From e4a599a9d37b5e7e1f7f947bde1be01674fd7a2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Sep 2016 10:14:22 +0200 Subject: [PATCH 426/701] --- .../y/Yade/Yade-2016.06a_include-signal.patch | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yade/Yade-2016.06a_include-signal.patch diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a_include-signal.patch b/easybuild/easyconfigs/y/Yade/Yade-2016.06a_include-signal.patch new file mode 100644 index 0000000000..28ff927ab4 --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a_include-signal.patch @@ -0,0 +1,10 @@ +--- trunk-2016.06a/py/wrapper/yadeWrapper.cpp.orig 2016-09-06 20:32:45.079249073 +0200 ++++ trunk-2016.06a/py/wrapper/yadeWrapper.cpp 2016-09-06 20:32:59.049059903 +0200 +@@ -39,6 +39,7 @@ + + #include + #include ++#include + + namespace py = boost::python; + -- GitLab From 05a4c417dbaf99c1c3ae8cb37add3748f835bd35 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 7 Sep 2016 10:39:44 +0200 Subject: [PATCH 427/701] flex has an M4 dependency --- easybuild/easyconfigs/f/flex/flex-2.6.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb index e7580df4ae..08a404a4b8 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] moduleclass = 'lang' -- GitLab From b5299437a92fe3312d002c7c19af81e77e9263d2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 7 Sep 2016 11:11:15 +0200 Subject: [PATCH 428/701] Add intel/2017 stuff --- .../i/icc/icc-2017.0.35-GCC-5.4.0-2.26.eb | 33 +++++++++++++++++ .../iccifort-2017.0.35-GCC-5.4.0-2.26.eb | 18 ++++++++++ .../i/ifort/ifort-2017.0.35-GCC-5.4.0-2.26.eb | 33 +++++++++++++++++ .../i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb | 20 +++++++++++ ...-2017.0.98-iimpi-2017.00-GCC-5.4.0-2.26.eb | 36 +++++++++++++++++++ ....0.98-iccifort-2017.0.35-GCC-5.4.0-2.26.eb | 35 ++++++++++++++++++ 6 files changed, 175 insertions(+) create mode 100644 easybuild/easyconfigs/i/icc/icc-2017.0.35-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2017.0.35-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2017.0.35-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.0.98-iimpi-2017.00-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2017.0.98-iccifort-2017.0.35-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.35-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.35-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..0c1088585e --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.35-GCC-5.4.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2017.0.35' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] + +checksums = ['c8a2fdb1501fbc93bfaad93195677d86'] + +gccver = '5.4.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.35-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.35-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..380fc915c1 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.35-GCC-5.4.0-2.26.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iccifort' +version = '2017.0.35' +versionsuffix = '-GCC-5.4.0-2.26' + +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, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.35-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.35-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..3b5cada858 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.35-GCC-5.4.0-2.26.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2017.0.35' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] + +checksums = ['8787795951fe10f90ce7dcdcec1b9341'] + +gccver = '5.4.0' +binutilsver = '2.26' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..b6b55ee8dc --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2017.00' +versionsuffix = '-GCC-5.4.0-2.26' + +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'} + +compver = '2017.0.35' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '2017.0.98', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.98-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.98-iimpi-2017.00-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..39201957df --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.98-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '2017.0.98' + +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': '2017.00-GCC-5.4.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['3cdcb739ab5ab1e047eb130b9ffdd8d0'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.0.98-iccifort-2017.0.35-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.98-iccifort-2017.0.35-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..109a0bb59e --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.98-iccifort-2017.0.35-GCC-5.4.0-2.26.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '2017.0.98' + +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': '2017.0.35-GCC-5.4.0-2.26'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['fc123875773816b7084a91e419d54d20'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' -- GitLab From 749d56ab211ddd8057a56eea9b420c6044060299 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Sep 2016 11:36:33 +0200 Subject: [PATCH 429/701] Eigen is just a build dep --- .../y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb index a7a4e68aef..c741427654 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb @@ -19,7 +19,6 @@ patches = ['Yade-%(version)s_include-signal.patch'] dependencies = [ ('Boost', '1.61.0', versionsuffix), ('CGAL', '4.8.1', versionsuffix), - ('Eigen', '3.2.9'), ('GDB', '7.11.1', versionsuffix), ('GL2PS', '1.3.9'), ('GTS', '0.7.6'), @@ -36,7 +35,10 @@ dependencies = [ ('zlib', '1.2.8'), ] -builddependencies = [('CMake', '3.6.1')] +builddependencies = [ + ('CMake', '3.6.1'), + ('Eigen', '3.2.9'), +] separate_build_dir = True -- GitLab From aa186c651730bde4c29415be4336de340d54b097 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 7 Sep 2016 13:02:40 +0200 Subject: [PATCH 430/701] FFmpeg 3.0.2 compiled using the foss 2016a toolchain. --- .../f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb new file mode 100644 index 0000000000..ee76ecf0f8 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.01'), + ('zlib', '1.2.8'), + ('x264', '20160430'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +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 [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' -- GitLab From a24fb94313549008275572cb13f21b3cddd2f925 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 7 Sep 2016 13:09:25 +0200 Subject: [PATCH 431/701] Statically link ncurses... so it's not needed at runtime --- easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb index b4e0ad7225..08e21adb47 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb @@ -16,7 +16,10 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['lua-%s.tar.gz' % version.replace('-', '.')] source_urls = ['http://sourceforge.net/projects/lmod/files/'] -dependencies = [('ncurses', '6.0')] +builddependencies = [('ncurses', '6.0')] + +# Use static linking for ncurses so it's not a runtime dep +configopts = "--with-static=yes" sanity_check_paths = { 'files': ["bin/lua"], -- GitLab From 19f0b03e3db99984c2786aa7afdda9a6d23ef0ee Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 7 Sep 2016 13:20:20 +0200 Subject: [PATCH 432/701] Remove versionmajor --- .../easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb index 6cc9d5dd83..5f366cc75c 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.7-foss-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ configopts = "configure.py --confirm-license" configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " configopts += " --no-sip-files" -options = {'modulename': '%(name)s%(version_major)s'} +options = {'modulename': '%(name)s'} modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -- GitLab From 32669a4f286050f00bef6cb0603495d489b26e27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Sep 2016 14:54:03 +0200 Subject: [PATCH 433/701] add easyconfig MATLAB-2016a.eb --- .../easyconfigs/m/MATLAB/MATLAB-2016a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb new file mode 100644 index 0000000000..e0113113d0 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb @@ -0,0 +1,20 @@ +name = 'MATLAB' +version = '2016a' + +homepage = 'http://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8.0_92')] + +import os +license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') +license_server_port = os.getenv('EB_MATLAB_LICENSE_SERVER_PORT', '00000') +key = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000') + +moduleclass = 'math' -- GitLab From 87102006dd97c02ed329be8ba8406fd2f617d478 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 7 Sep 2016 15:37:55 +0200 Subject: [PATCH 434/701] Added bzip2 and libxcb dependencies, which are pulled in by FFmpeg if available. --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb | 2 ++ easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb | 2 ++ easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb | 4 +++- 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb index ee76ecf0f8..4eee74c062 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-foss-2016a.eb @@ -14,7 +14,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.12.01'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160430'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb index fb0c75a29b..e54dddf525 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb @@ -14,7 +14,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.12.01'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160430'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb index 4dee167c84..ee98b51ed2 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb @@ -12,9 +12,11 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ - ('NASM', '2.12.02'), + ('NASM', '2.12.01'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160614'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -- GitLab From 4e48ef9ed080c2fea438d27d1c1ed0441fd89d81 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 7 Sep 2016 15:40:10 +0200 Subject: [PATCH 435/701] Replaced 'so' by SHLIB_EXT --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb index e54dddf525..fd22efefe0 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.0.2-intel-2016a.eb @@ -25,7 +25,7 @@ configopts += '--enable-libx264' 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']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb index ee98b51ed2..07da64a12f 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb @@ -25,7 +25,7 @@ configopts += '--enable-libx264' 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']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } -- GitLab From e7b4997128a920299cdc321af07fd75596fb28ea Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 7 Sep 2016 15:44:02 +0200 Subject: [PATCH 436/701] Undid an accidental version change in NASM. --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb index 07da64a12f..55a07fcd2a 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ - ('NASM', '2.12.01'), + ('NASM', '2.12.02'), ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('x264', '20160614'), -- GitLab From 0b2586a18f6c528a97505b9061cf26c11edec606 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 7 Sep 2016 15:53:50 +0200 Subject: [PATCH 437/701] Changed libxcb into X11, which includes libxcb. --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb index 55a07fcd2a..53b2bbfa0a 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb @@ -16,7 +16,7 @@ dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('x264', '20160614'), - ('libxcb', '1.11.1'), + (('X11', '20160819'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -- GitLab From ee63f8258b912c1424bb1b3b2ae262cc7590fd4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Sep 2016 16:01:19 +0200 Subject: [PATCH 438/701] add easyconfig PIL-1.1.7-intel-2016b-Python-2.7.12.eb --- .../PIL-1.1.7-intel-2016b-Python-2.7.12.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1e4d5e4103 --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('libjpeg-turbo', '1.5.0'), + ('freetype', '2.6.5'), +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' -- GitLab From d802e6b9ce5116ac0f7c44e1c230c173ba0a11e3 Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 7 Sep 2016 16:07:39 +0200 Subject: [PATCH 439/701] Add M4 as a dep of flex, this is required by some config processes when working with lex --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb | 5 ++++- easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb | 5 ++++- 14 files changed, 56 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb index 3626cfd239..9a286850a4 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index 4015f41291..155b9e6155 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb index 0b38c37169..d1a9375e34 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index e1a9437774..d5c3db995c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb index 299747415e..2801060df2 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb index 687cf19d5f..a0f6f0c641 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.27', '', True)] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb index 76aba74a8b..239f478236 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.27', '', True)] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb index bd783441d3..621cdb0aaf 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb index 13ec4d5ea6..5969d1e4b9 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb index a59cd4005e..d24b602e70 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb index c2677565b5..e6510e7ef7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb index c3e7a6b965..59f659121c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb index f451c3ed90..ee500a048e 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb index 39937675eb..acc1431c3f 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [('Bison', '3.0.4')] +dependencies = [ + ('Bison', '3.0.4'), + ('M4', '1.4.17') +] moduleclass = 'lang' -- GitLab From 22f35e4292e5760dc0b04b4ade83a6c9d6371b50 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 7 Sep 2016 16:21:40 +0200 Subject: [PATCH 440/701] Fixed typo. --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb index 53b2bbfa0a..0744eae109 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb @@ -16,7 +16,7 @@ dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('x264', '20160614'), - (('X11', '20160819'), + ('X11', '20160819'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -- GitLab From a22bc690d3a64cf393d846c18c4c4220ed6e3cd0 Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 7 Sep 2016 16:30:47 +0200 Subject: [PATCH 441/701] Add libreadline dep to Lua for static build --- easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb | 5 ++- .../l/libreadline/libreadline-6.3.eb | 31 +++++++++++++++++++ 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb index 08e21adb47..08d864aaf6 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb @@ -16,7 +16,10 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['lua-%s.tar.gz' % version.replace('-', '.')] source_urls = ['http://sourceforge.net/projects/lmod/files/'] -builddependencies = [('ncurses', '6.0')] +builddependencies = [ + ('ncurses', '6.0'), + ('libreadline', '6.3') +] # Use static linking for ncurses so it's not a runtime dep configopts = "--with-static=yes" diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb new file mode 100644 index 0000000000..53eeab2af9 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb @@ -0,0 +1,31 @@ +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': 'dummy', 'version': ''} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +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 f2e026ccce99dd60f6d44e74000ac3f9007c5e84 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 7 Sep 2016 16:52:22 +0200 Subject: [PATCH 442/701] Added zlib2 and libxcb as dependencies. Changed 'so' into SHLIB_EXT. --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb | 4 +++- easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb | 4 +++- easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb | 2 ++ easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb | 4 +++- 4 files changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb index 3e71d0c50e..36e057b469 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-0.10.16-intel-2016a.eb @@ -16,7 +16,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.11.08'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160114'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' @@ -25,7 +27,7 @@ configopts += '--enable-libx264' 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']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb index 40be8fe314..3349ed3961 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.6-intel-2016a.eb @@ -14,7 +14,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.11.08'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160114'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' @@ -23,7 +25,7 @@ configopts += '--enable-libx264' 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']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb index 0badebf4eb..8664387506 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-foss-2016a.eb @@ -14,7 +14,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.12.01'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160430'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb index 05478ccada..c6c61c7b35 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-2.8.7-intel-2016a.eb @@ -14,7 +14,9 @@ source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ ('NASM', '2.12.01'), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ('x264', '20160430'), + ('libxcb', '1.11.1'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' @@ -23,7 +25,7 @@ configopts += '--enable-libx264' 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']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } -- GitLab From 45c4c8e9b9485e25500fff7fc2f315c3108d2c4e Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 7 Sep 2016 17:31:05 +0200 Subject: [PATCH 443/701] Add pkg-config to solve libtinfo problem related to ncurses --- easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb | 1 + .../l/libreadline/libreadline-6.3.eb | 1 + .../easyconfigs/n/ncurses/ncurses-6.0.eb | 2 ++ .../p/pkg-config/pkg-config-0.29.eb | 27 +++++++++++++++++++ 4 files changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb index 08d864aaf6..8a6c29fb66 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb @@ -17,6 +17,7 @@ sources = ['lua-%s.tar.gz' % version.replace('-', '.')] source_urls = ['http://sourceforge.net/projects/lmod/files/'] builddependencies = [ + ('pkg-config', '0.29'), ('ncurses', '6.0'), ('libreadline', '6.3') ] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb index 53eeab2af9..323eaa8c72 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb @@ -16,6 +16,7 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] patches = ['libreadline-%(version)s-bugfix.patch'] +builddependencies = [('pkg-config', '0.29')] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 51d2a6f539..0709b71444 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +builddependencies = [('pkg-config', '0.29')] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.eb new file mode 100644 index 0000000000..4302c5e3ae --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29' + +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).""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 81c99726ddb1e84b1866404c7166c648d2741840 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2016 09:20:26 +0200 Subject: [PATCH 444/701] add easyconfig POV-Ray-3.7.0.0-intel-2016b.eb, add easyconfig SDL2-2.0.4-intel-2016b.eb --- .../p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb | 56 +++++++++++++++++++ .../POV-Ray-3.7.0.0_fix-boost-linking.patch | 30 ++++++++++ .../s/SDL2/SDL2-2.0.4-intel-2016b.eb | 35 ++++++++++++ 3 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0_fix-boost-linking.patch create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb new file mode 100644 index 0000000000..b01bff9fa6 --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb @@ -0,0 +1,56 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, 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 = 'POV-Ray' +version = '3.7.0.0' + +homepage = 'http://www.povray.org/' +description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program + which generates images from a text-based scene description, and is available for a variety + of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning + three-dimensional graphics. The source code is available for those wanting to do their own ports.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/POV-Ray/povray/archive/'] +patches = ['POV-Ray-%(version)s_fix-boost-linking.patch'] + +dependencies = [ + ('Boost', '1.61.0'), + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('X11', '20160819'), + ('LibTIFF', '4.0.6'), + ('SDL2', '2.0.4'), +] +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " +preconfigopts += " ./prebuild.sh && cd .. && " +configopts = "COMPILED_BY='EasyBuild' " +configopts += "--with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB --with-libpng=$EBROOTLIBPNG " +configopts += "--with-libtiff=$EBROOTLIBTIFF --with-libjpeg=$EBROOTLIBJPEGMINTURBO --with-libsdl=$EBROOTSDL2 " +# configopts += " --with-libmkl=DIR " ## upstream needs to fix this, still in BETA + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/povray'], + 'dirs': ['etc/povray/%(version_major_minor)s', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0_fix-boost-linking.patch b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0_fix-boost-linking.patch new file mode 100644 index 0000000000..aac9faf990 --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0_fix-boost-linking.patch @@ -0,0 +1,30 @@ +also include -lboost_system when linking with -lboost_thread +cfr. https://build.opensuse.org/package/view_file/openSUSE:Leap:42.1:NonFree/povray/povray-3.6.9.7-boost-link.patch?expand=1 +--- povray-3.7.0.0/unix/config/ax_boost_thread.m4.orig 2013-11-06 21:28:15.000000000 +0100 ++++ povray-3.7.0.0/unix/config/ax_boost_thread.m4 2016-09-07 18:26:36.447847499 +0200 +@@ -104,14 +104,14 @@ + for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + if test "x$link_thread" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/boost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + fi +@@ -119,7 +119,7 @@ + else + for ax_lib in $ax_boost_user_thread_lib boost_thread-$ax_boost_user_thread_lib; do + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb new file mode 100644 index 0000000000..b1bfaa43d3 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, 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 = 'SDL2' +version = '2.0.4' + +homepage = 'http://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Yasm', '1.3.0')] + +configopts = ' --disable-nasm --without-x ' + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 66405bd372a5472e691fab9e7e8637af6cc7ec23 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Thu, 8 Sep 2016 09:53:26 +0200 Subject: [PATCH 445/701] Version of OpenCV using the foss 2016a toolchain. Gstreamer has been added as an extra dependency compared to the intel 2016a toolchain. --- .../o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb new file mode 100644 index 0000000000..f835d278f9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -0,0 +1,67 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.1.0' + +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': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/Itseez/opencv/archive/'] +sources = ['%(version)s.zip'] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +dependencies = [ + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('FFmpeg', '3.0.2'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), + ('libpng', '1.6.21'), + ('LibTIFF', '4.0.6'), + ('JasPer', '1.900.1'), + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('GLib', '2.48.0'), + ('GTK+', '2.24.30'), + ('GStreamer', '1.6.4'), + ('GST-plugins-base', '1.6.4'), +] + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$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.%s' % SHLIB_EXT ] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' -- GitLab From df85fb067a882bf3dcbf91742af583b832ba1a55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2016 10:09:50 +0200 Subject: [PATCH 446/701] add easyconfig Blender-2.77a-intel-2016b-Python-3.5.2.eb, add easyconfig OpenImageIO-1.6.17-intel-2016b.eb, add easyconfig OpenEXR-2.2.0-intel-2016b.eb --- .../Blender-2.77a-intel-2016b-Python-3.5.2.eb | 51 +++++++++++++++++++ .../Blender-2.77a_fix-ARRAY_SIZE-icc.patch | 13 +++++ .../o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb | 32 ++++++++++++ .../OpenImageIO-1.6.17-intel-2016b.eb | 32 ++++++++++++ 4 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/b/Blender/Blender-2.77a_fix-ARRAY_SIZE-icc.patch create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.6.17-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..88adcef860 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'Blender' +version = '2.77a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://download.blender.org/source/'] +patches = ['Blender-%(version)s_fix-ARRAY_SIZE-icc.patch'] + +# These are needed until extra dependencies are added for them to work +configopts = '-DWITH_INSTALL_PORTABLE=OFF ' +configopts += '-DWITH_BUILDINFO=OFF ' +configopts += '-DWITH_GAMEENGINE=OFF ' +#configopts += '-DWITH_CYCLES=OFF ' +configopts += '-DWITH_SYSTEM_GLEW=OFF ' + +# Python paths +configopts += '-DPYTHON_VERSION=%(pyshortver)s -DPYTHON_LIBRARY=${EBROOTPYTHON}/lib/libpython%(pyshortver)sm.so ' +configopts += '-DPYTHON_INCLUDE_DIR=${EBROOTPYTHON}/include/python%(pyshortver)sm ' +configopts += '-DOPENEXR_INCLUDE_DIR=$EBROOTOPENEXR/include ' + +dependencies = [ + ('Python', '3.5.2'), + ('Boost', '1.61.0'), + ('libjpeg-turbo', '1.5.0'), + ('zlib', '1.2.8'), + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('OpenImageIO', '1.6.17'), # required for cycles render engine +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = 'True' + +modextravars = {'GALLIUM_DRIVER': 'swr'} + +sanity_check_paths = { + 'files': ['bin/blender'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a_fix-ARRAY_SIZE-icc.patch b/easybuild/easyconfigs/b/Blender/Blender-2.77a_fix-ARRAY_SIZE-icc.patch new file mode 100644 index 0000000000..2cc57b24de --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a_fix-ARRAY_SIZE-icc.patch @@ -0,0 +1,13 @@ +use simple definition of ARRAY_SIZE macro when using Intel compilers +author: Kenneth Hoste (HPC-UGent) +--- blender-2.77a/source/blender/blenlib/BLI_utildefines.h.orig 2016-09-07 14:21:00.287130174 +0200 ++++ blender-2.77a/source/blender/blenlib/BLI_utildefines.h 2016-09-07 14:21:08.087031653 +0200 +@@ -435,7 +435,7 @@ + } (void)0 + + /* assuming a static array */ +-#if defined(__GNUC__) && !defined(__cplusplus) && !defined(__clang__) ++#if defined(__GNUC__) && !defined(__cplusplus) && !defined(__clang__) && !defined(__INTEL_COMPILER) + # define ARRAY_SIZE(arr) \ + ((sizeof(struct {int isnt_array : ((const void *)&(arr) == &(arr)[0]);}) * 0) + \ + (sizeof(arr) / sizeof(*(arr)))) diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb new file mode 100644 index 0000000000..479f9021ce --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '2.2.0' + +homepage = 'http://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/openexr/openexr/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.6.1')] + +env_vars = "CPATH=%(installdir)s/include/OpenEXR:$CPATH " +env_vars += "LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH " +env_vars += "LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH" +preconfigopts = [ + "cd IlmBase && ", + "cd OpenEXR && " + env_vars, +] +prebuildopts = preconfigopts[:] +preinstallopts = preconfigopts[:] + +sanity_check_paths = { + 'files': ['lib/libHalf.so'], + 'dirs': ['bin', 'include/OpenEXR', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.6.17-intel-2016b.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.6.17-intel-2016b.eb new file mode 100644 index 0000000000..7e6e2a6a22 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.6.17-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '1.6.17' + +homepage = 'http://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] +sources = ['Release-%(version)s.tar.gz'] + +dependencies = [ + ('Boost', '1.61.0'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), + ('OpenEXR', '2.2.0'), +] +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.so', 'lib/libOpenImageIO_Util.so'], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' -- GitLab From 5e436c74010cf65b8c43ffcda70326bf91db2ae5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2016 10:25:49 +0200 Subject: [PATCH 447/701] fix remarks, drop Yasm build dep since it's not required --- easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb index b1bfaa43d3..9d089f04eb 100644 --- a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb @@ -23,9 +23,9 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.libsdl.org/release/'] sources = [SOURCE_TAR_GZ] -builddependencies = [('Yasm', '1.3.0')] - -configopts = ' --disable-nasm --without-x ' +dependencies = [ + ('X11', '20160819'), +] sanity_check_paths = { 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], -- GitLab From e6c16c0060ad11f6f4ce3baba0c6de64acbd4ca8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2016 11:00:50 +0200 Subject: [PATCH 448/701] drop commented out configure option --- .../b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb index 88adcef860..e84bfbddb5 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb @@ -19,7 +19,6 @@ patches = ['Blender-%(version)s_fix-ARRAY_SIZE-icc.patch'] configopts = '-DWITH_INSTALL_PORTABLE=OFF ' configopts += '-DWITH_BUILDINFO=OFF ' configopts += '-DWITH_GAMEENGINE=OFF ' -#configopts += '-DWITH_CYCLES=OFF ' configopts += '-DWITH_SYSTEM_GLEW=OFF ' # Python paths -- GitLab From ea7488eb266804bc9084643e1538668d24bdef33 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 8 Sep 2016 11:43:58 +0200 Subject: [PATCH 449/701] Add scikit-learn/0.17.1-intel-2016b-Python-2.7.12 --- ...-learn-0.17.1-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..8bee613d8e --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.17.1' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.2', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 351c4a1f74acfba899d222b9b555c8b29a1d31c5 Mon Sep 17 00:00:00 2001 From: Alan Date: Wed, 7 Sep 2016 17:31:05 +0200 Subject: [PATCH 450/701] Add configure option to solve libtinfo problem related to ncurses --- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 51d2a6f539..fc2dde62d1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -16,9 +16,9 @@ sources = [SOURCE_TAR_GZ] configopts = [ # default build - '--with-shared --enable-overwrite', + '--with-shared --enable-overwrite --with-termlib', # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --with-termlib ' + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] libs = ["form", "menu", "ncurses", "panel"] -- GitLab From 070f0a553c4b04f292e57bba58e3910fc9c0ff4b Mon Sep 17 00:00:00 2001 From: Alan Date: Thu, 8 Sep 2016 12:14:24 +0200 Subject: [PATCH 451/701] Make ncurses build the terminfo library separately --- easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb | 1 - .../l/libreadline/libreadline-6.3.eb | 1 - .../easyconfigs/n/ncurses/ncurses-6.0.eb | 5 ++-- .../p/pkg-config/pkg-config-0.29.eb | 27 ------------------- 4 files changed, 2 insertions(+), 32 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb index 8a6c29fb66..08d864aaf6 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb @@ -17,7 +17,6 @@ sources = ['lua-%s.tar.gz' % version.replace('-', '.')] source_urls = ['http://sourceforge.net/projects/lmod/files/'] builddependencies = [ - ('pkg-config', '0.29'), ('ncurses', '6.0'), ('libreadline', '6.3') ] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb index 323eaa8c72..53eeab2af9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb @@ -16,7 +16,6 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] patches = ['libreadline-%(version)s-bugfix.patch'] -builddependencies = [('pkg-config', '0.29')] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 657d0d5f9b..f923e1597d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -14,13 +14,12 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -builddependencies = [('pkg-config', '0.29')] - configopts = [ # default build '--with-shared --enable-overwrite --with-termlib', # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --with-termlib ' + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --with-termlib ' + + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] libs = ["form", "menu", "ncurses", "panel"] diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.eb deleted file mode 100644 index 4302c5e3ae..0000000000 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pkg-config' -version = '0.29' - -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).""" - -toolchain = {'name': 'dummy', 'version': ''} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] - -# don't use PAX, it might break. -tar_config_opts = True - -configopts = " --with-internal-glib" - -sanity_check_paths = { - 'files': ['bin/pkg-config'], - 'dirs': [], -} - -moduleclass = 'devel' -- GitLab From fa54afe020c934bb241257524dfb3d47ef9f98c3 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 8 Sep 2016 12:18:39 +0200 Subject: [PATCH 452/701] Check for terminfo libs during sanitycheck --- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index f923e1597d..dcca941e16 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -22,7 +22,7 @@ configopts = [ '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] -libs = ["form", "menu", "ncurses", "panel"] +libs = ["form", "menu", "ncurses", "panel", "tinfo"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + -- GitLab From e838908a96e98f0da99fffca7f0467aabf53c4f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2016 13:03:50 +0200 Subject: [PATCH 453/701] make sure & check that Graphviz does not install Tcl bindings in Tcl install prefix --- .../easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb | 5 ++++- .../g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb index aee7aa31e0..3c2e6fe51b 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb @@ -50,13 +50,16 @@ configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' configopts += '--enable-r=no --enable-ruby=no ' prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' +buildopts = "TCL_INSTALL_DIR=/dev/null" sanity_check_paths = { 'files': ['bin/cluster', 'bin/dot', 'bin/gvmap', 'lib/libcdt.%s' % SHLIB_EXT, 'lib/libgvc.%s' % SHLIB_EXT, 'lib/libxdot.%s' % SHLIB_EXT], - 'dirs': ['include'] + 'dirs': ['include', 'lib/graphviz'] } +sanity_check_commands = [("test ! -d $EBROOTTCL/lib64/*/graphviz", '')] + modextrapaths = { 'PYTHONPATH': 'lib/graphviz/python', 'CLASSPATH': 'lib/graphviz/java/org/graphviz', diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index 231a5ddb6f..2d50c9c33c 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -52,13 +52,16 @@ configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' configopts += '--enable-r=no --enable-ruby=no ' prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' +buildopts = "TCL_INSTALL_DIR=/dev/null" sanity_check_paths = { 'files': ['bin/cluster', 'bin/dot', 'bin/gvmap', 'lib/libcdt.%s' % SHLIB_EXT, 'lib/libgvc.%s' % SHLIB_EXT, 'lib/libxdot.%s' % SHLIB_EXT], - 'dirs': ['include'] + 'dirs': ['include', 'lib/graphviz'] } +sanity_check_commands = [("test ! -d $EBROOTTCL/lib64/*/graphviz", '')] + modextrapaths = { 'PYTHONPATH': 'lib/graphviz/python', 'CLASSPATH': 'lib/graphviz/java/org/graphviz', -- GitLab From 7a7f98d707ec045983fdd14b2af127b99666099c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2016 14:24:53 +0200 Subject: [PATCH 454/701] add easyconfig SimVascular-2.16.0406-intel-2016b.eb --- .../SimVascular-2.16.0406-intel-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb b/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb new file mode 100644 index 0000000000..ee1b07c5d3 --- /dev/null +++ b/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'SimVascular' +version = '2.16.0406' + +homepage = 'http://simvascular.github.io/' +description = """SimVascular is an open source software suite for cardiovascular simulation, providing a complete + pipeline from medical image data to 3D model construction, meshing, and blood flow simulation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# downlaod via https://simtk.org/project/xml/downloads.xml?group_id=188 +sources = ['SV-linux-x64-2016-04-06.tar.gz'] + +dependencies = [ + ('X11', '20160819'), + ('Tcl', '8.6.5'), + ('Tk', '8.6.5', '-no-X11'), +] + +unpack_options = '--strip-components=1' +keepsymlinks = True + +# mimic what setup-symlinks.sh, but stick to dedicated install dir +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "ln -s %(installdir)s/Bin/simvascular %(installdir)s/bin/simvascular", + "ln -s %(installdir)s/Bin/svpost %(installdir)s/bin/svpost", + "ln -s %(installdir)s/Bin/svpre %(installdir)s/bin/svpre", + "ln -s %(installdir)s/Bin/svsolver %(installdir)s/bin/svsolver", +] + +sanity_check_paths = { + 'files': ['bin/simvascular', 'bin/svpost', 'bin/svpre', 'bin/svsolver'], + 'dirs': ['Bin', 'lib'], +} + +moduleclass = 'bio' -- GitLab From 7855e21cc4821d83fe0c241b783f55efe5adaf2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2016 14:31:29 +0200 Subject: [PATCH 455/701] fix Tk dep, no versionsuffix --- .../s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb b/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb index ee1b07c5d3..292413c3e2 100644 --- a/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb @@ -15,7 +15,7 @@ sources = ['SV-linux-x64-2016-04-06.tar.gz'] dependencies = [ ('X11', '20160819'), ('Tcl', '8.6.5'), - ('Tk', '8.6.5', '-no-X11'), + ('Tk', '8.6.5'), ] unpack_options = '--strip-components=1' -- GitLab From 543f6b31925df67cb2e0149397ff6021bb85f0d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2016 14:35:21 +0200 Subject: [PATCH 456/701] fix remarks --- .../s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb b/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb index 292413c3e2..6727139e3e 100644 --- a/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SimVascular/SimVascular-2.16.0406-intel-2016b.eb @@ -9,7 +9,7 @@ description = """SimVascular is an open source software suite for cardiovascular toolchain = {'name': 'intel', 'version': '2016b'} -# downlaod via https://simtk.org/project/xml/downloads.xml?group_id=188 +# download via https://simtk.org/project/xml/downloads.xml?group_id=188 sources = ['SV-linux-x64-2016-04-06.tar.gz'] dependencies = [ @@ -32,7 +32,7 @@ postinstallcmds = [ sanity_check_paths = { 'files': ['bin/simvascular', 'bin/svpost', 'bin/svpre', 'bin/svsolver'], - 'dirs': ['Bin', 'lib'], + 'dirs': ['Bin'], } moduleclass = 'bio' -- GitLab From 2b4db2bf68835fd00656f1edb34f00ab8bfbf5f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2016 14:40:05 +0200 Subject: [PATCH 457/701] patch tclpkg/Makefile.in to avoid installing Graphviz bindings to non-owned directories --- easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb | 2 +- .../g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb index 3c2e6fe51b..c85ed5ed21 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb @@ -46,11 +46,11 @@ patches = [ 'Graphviz-2.38.0_icc_sfio.patch', ] +preconfigopts = "sed -i 's/install-data-hook$//g' tclpkg/Makefile.in && " configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' configopts += '--enable-r=no --enable-ruby=no ' prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' -buildopts = "TCL_INSTALL_DIR=/dev/null" sanity_check_paths = { 'files': ['bin/cluster', 'bin/dot', 'bin/gvmap', diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index 2d50c9c33c..88594633da 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -48,11 +48,11 @@ patches = [ 'Graphviz-2.38.0_icc_sfio.patch', ] +preconfigopts = "sed -i 's/install-data-hook$//g' tclpkg/Makefile.in && " configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' configopts += '--enable-r=no --enable-ruby=no ' prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' -buildopts = "TCL_INSTALL_DIR=/dev/null" sanity_check_paths = { 'files': ['bin/cluster', 'bin/dot', 'bin/gvmap', -- GitLab From b53b2802faf0fa4e37760c3542fe3d458d6e4a0c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 9 Sep 2016 10:55:58 +0800 Subject: [PATCH 458/701] rename spglib to spglib-python --- ...ymatgen-4.1.1-intel-2016b-Python-2.7.12.eb | 2 +- ...ython-1.9.4.2-intel-2016b-Python-2.7.12.eb | 26 +++++++++++++++++++ 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb index 21004fbe46..6b8241e929 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.1.1-intel-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.12'), - ('spglib', '1.9.4.2', versionsuffix), + ('spglib-python', '1.9.4.2', versionsuffix), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0545ab1823 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'spglib-python' +version = '1.9.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://files.pythonhosted.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' -- GitLab From 827d74b24e0fabd96a608708ed51e9196febba9e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 9 Sep 2016 17:30:59 +0800 Subject: [PATCH 459/701] revert to pypi.python.org source_url --- .../spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb index 0545ab1823..2cbf7eff9e 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.4.2-intel-2016b-Python-2.7.12.eb @@ -9,7 +9,7 @@ description = """Spglib for Python. Spglib is a library for finding and handling toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https://files.pythonhosted.org/packages/source/%(nameletter)s/spglib'] +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] sources = ['spglib-%(version)s.tar.gz'] dependencies = [ -- GitLab From e15727dac4cb0a08ef7d933868ff6a0a5670a7c6 Mon Sep 17 00:00:00 2001 From: Arif Ali Date: Fri, 9 Sep 2016 10:17:14 +0100 Subject: [PATCH 460/701] fix python 3.5.2 compilation with various toolchains --- easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb | 6 ++++++ 3 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb index 2581a2015d..f49b2ff085 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.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', + ], }), ('pbr', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -76,6 +79,9 @@ 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', '4.0.10', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb index 33f145a36c..f40c4aab55 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.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', + ], }), ('pbr', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -76,6 +79,9 @@ 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', '4.0.10', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb index 4cba8641bb..805061ab30 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.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', + ], }), ('pbr', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -76,6 +79,9 @@ 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', '4.0.10', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], -- GitLab From db3480158565ed5f9112cb525d1ff5739de9474d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Sep 2016 12:04:52 +0200 Subject: [PATCH 461/701] make sure EasyBuild is in full control over optimization flags in Blender easyconfig --- .../b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb index e84bfbddb5..1ddf498f76 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.77a-intel-2016b-Python-3.5.2.eb @@ -15,8 +15,11 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://download.blender.org/source/'] patches = ['Blender-%(version)s_fix-ARRAY_SIZE-icc.patch'] -# These are needed until extra dependencies are added for them to work -configopts = '-DWITH_INSTALL_PORTABLE=OFF ' +# disable SSE detection to give EasyBuild full control over optimization compiler flags being used +configopts = '-DWITH_CPU_SSE=OFF -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG" -DCMAKE_CXX_FLAGS_RELEASE="-DNDEBUG" ' + +# these are needed until extra dependencies are added for them to work +configopts += '-DWITH_INSTALL_PORTABLE=OFF ' configopts += '-DWITH_BUILDINFO=OFF ' configopts += '-DWITH_GAMEENGINE=OFF ' configopts += '-DWITH_SYSTEM_GLEW=OFF ' -- GitLab From 08fc54841a76c32e98efdd1f259f73adacf2eb22 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Sep 2016 13:42:23 +0200 Subject: [PATCH 462/701] stick to matplotlib 1.5.1 in scikit-learn, for compatibility with other Python modules --- .../scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb index 8bee613d8e..948220fce8 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-intel-2016b-Python-2.7.12.eb @@ -17,7 +17,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.12'), - ('matplotlib', '1.5.2', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix), ] options = {'modulename': 'sklearn'} -- GitLab From 8a3cb590b859f77ab79d6e58c7073a86f53de7d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Sep 2016 17:20:49 +0200 Subject: [PATCH 463/701] add easyconfig GRIT-2.0.5-intel-2016b-Python-2.7.12.eb --- .../GRIT-2.0.5-intel-2016b-Python-2.7.12.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2da2d712ac --- /dev/null +++ b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,41 @@ +easyblock = 'Bundle' + +name = 'GRIT' +version = '2.0.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nboley/grit' +description = """GRIT - A tool for the integrative analysis of RNA-seq type assays""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), +] + +exts_list = [ + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + }), + ('pysam', '0.9.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pysam/'], + }), + (name, version, { + 'source_urls': ['https://github.com/nboley/grit/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/run_grit'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('run_grit', '--help')] + +moduleclass = 'bio' -- GitLab From 6fc007377280cd9031b791f0aa07ca0a15490fc4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Sep 2016 18:54:58 +0200 Subject: [PATCH 464/701] add easyconfig hanythingondemand-3.1.4-cli.eb, add easyconfig hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb --- .../hanythingondemand-3.1.4-cli.eb | 42 +++++++++++++++++++ ...ndemand-3.1.4-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb new file mode 100644 index 0000000000..275b2940c7 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.4' +versionsuffix = '-cli' + +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': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) +dependencies = [ + ('pbs_python', '4.6.0'), + ('vsc-base', '2.5.1'), +] + +use_easy_install = True +zipped_egg = True + +# use 'hod' rather than 'hanythingondemand' in module name +modaltsoftname = 'hod' + +options = {'modulename': 'hod'} + +modextravars = { + # site-specific settings, hence commented out + # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) + #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # specify location on shared 'scratch' filesystem for HOD working directories + #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f133f273c4 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.4' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime +dependencies = [ + ('Python', '2.7.12'), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.3', versionsuffix), +] + +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'hod'} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' -- GitLab From 1815dfecf67ec275c3873cd88a2985c845759e90 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 10 Sep 2016 11:54:12 +0800 Subject: [PATCH 465/701] delete renamed file --- ...pglib-1.9.4.2-intel-2016b-Python-2.7.12.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.9.4.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.9.4.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/spglib/spglib-1.9.4.2-intel-2016b-Python-2.7.12.eb deleted file mode 100644 index 9a2186080b..0000000000 --- a/easybuild/easyconfigs/s/spglib/spglib-1.9.4.2-intel-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'spglib' -version = '1.9.4.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/spglib' -description = """Spglib is a library for finding and handling crystal symmetries written in C.""" - -toolchain = {'name': 'intel', 'version': '2016b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.12'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - -moduleclass = 'chem' -- GitLab From 11d62c145dce95596d8a5d66ce4dc7db2c159a31 Mon Sep 17 00:00:00 2001 From: Bob Date: Mon, 12 Sep 2016 15:37:52 +0200 Subject: [PATCH 466/701] Remove old comment --- easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb index 572719879c..55e5aba8b6 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb @@ -12,7 +12,6 @@ homepage = 'http://cmpg.unibe.ch/software/BayeScan/' description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.""" -# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'openmp': True} -- GitLab From 18078071cb975bbdee8e737ac59e7e0870c38490 Mon Sep 17 00:00:00 2001 From: Bob Date: Mon, 12 Sep 2016 15:38:53 +0200 Subject: [PATCH 467/701] One file per line for files_to_copy --- .../easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb index 55e5aba8b6..c4932d3953 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb @@ -22,7 +22,12 @@ prebuildopts = "sed -i.bk 's/g++/${CXX} ${CXXFLAGS}/g' Makefile && " start_dir = 'source' -files_to_copy = [(['source/bayescan_%(version)s'], 'bin'), 'BayeScan%(version)s_manual.pdf' , 'input_examples', 'R functions'] +files_to_copy = [ + (['source/bayescan_%(version)s'], 'bin'), + 'BayeScan%(version)s_manual.pdf', + 'input_examples', + 'R functions' +] parallel = 1 -- GitLab From b7dc6b3f843846551af275bc67bb7aa293097a0e Mon Sep 17 00:00:00 2001 From: Bob Date: Mon, 12 Sep 2016 15:45:15 +0200 Subject: [PATCH 468/701] Use instead of -lopenblas -lgfortran --- .../easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb | 2 +- .../easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb index 91d5649298..97dd9ce1c7 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb @@ -31,7 +31,7 @@ dependencies = [ # -lm and -pthread are missing in the Makefile # also run "make install" after make to copy all binaries to the bin dir -buildopts = 'LDLIBS="-lgsl -lopenblas -lgfortran -lrt -lm" LDFLAGS="$LDFLAGS -pthread" && make install' +buildopts = 'LDLIBS="-lgsl $LIBBLAS -lrt -lm" LDFLAGS="$LDFLAGS -pthread" && make install' start_dir = 'src' diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb index 9d605117a0..db8b80af14 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb @@ -30,7 +30,8 @@ dependencies = [ ] # -lm and -pthread are missing in the Makefile -buildopts = 'LDLIBS="-lgsl -lopenblas -lgfortran -lrt -lm" LDFLAGS="$LDFLAGS -pthread" && make install' +# also run "make install" after make to copy all binaries to the bin dir +buildopts = 'LDLIBS="-lgsl $LIBBLAS -lrt -lm" LDFLAGS="$LDFLAGS -pthread" && make install' start_dir = 'src' -- GitLab From 6cac8f59db781c65839c08fa3bf95dce8b9d8d86 Mon Sep 17 00:00:00 2001 From: Bob Date: Mon, 12 Sep 2016 15:45:43 +0200 Subject: [PATCH 469/701] Minor style fix --- .../easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb | 3 ++- .../easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb index 97dd9ce1c7..653bc39a36 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb @@ -22,7 +22,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [ 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/', - 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/'] + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/' +] sources = ['EIG%(version)s.tar.gz'] dependencies = [ diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb index db8b80af14..90343733e3 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb @@ -22,7 +22,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [ 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/', - 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/'] + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/' +] sources = ['EIG%(version)s.tar.gz'] dependencies = [ -- GitLab From 0b6784a43bce3eff123fb5896b39d6bf8e644af6 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 12 Sep 2016 17:18:53 +0200 Subject: [PATCH 470/701] Version of protobuf using the foss 2016a toolchain. Since protobuf includes libraries, compiling it with the compiler from a toolchain seems better. --- .../p/protobuf/protobuf-3.0.2-foss-2016a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb new file mode 100644 index 0000000000..14ba425f1f --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.0.2' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] + +preconfigopts = "./autogen.sh &&" + +sanity_check_paths = { + 'files': ['bin/protoc','lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ca924569f9d349f04a988df49bafee28f82af7e7 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 13 Sep 2016 10:27:06 +0200 Subject: [PATCH 471/701] Python library for Google protobuf, compiled using foss 2016a. --- ...f-python-3.0.2-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ ...uf-python-3.0.2-foss-2016a-Python-3.5.1.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1ff4a4ad43 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.0.2' +versionsuffix= '-Python-%(version)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +versionsuffix = '-Python-%(pyver)s' + +dependencies = [ + ('Python', '2.7.11'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/protobuf-%(version)s-py%(pyshortver)s.egg/google/__init__.py'], + 'dirs': ['bin'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..2c3f2283d9 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.0.2' +versionsuffix= '-Python-%(version)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +versionsuffix = '-Python-%(pyver)s' + +dependencies = [ + ('Python', '3.5.1'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/protobuf-%(version)s-py%(pyshortver)s.egg/google/__init__.py'], + 'dirs': ['bin'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' -- GitLab From 21a129fac315efa3e51c4432dae006763c5a007e Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 12 Sep 2016 17:18:53 +0200 Subject: [PATCH 472/701] Version of protobuf using the foss 2016a toolchain. Since protobuf includes libraries, compiling it with the compiler from a toolchain seems better. --- .../p/protobuf/protobuf-3.0.2-foss-2016a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb new file mode 100644 index 0000000000..14ba425f1f --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.0.2-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.0.2' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] + +preconfigopts = "./autogen.sh &&" + +sanity_check_paths = { + 'files': ['bin/protoc','lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From e35203c16ecd51118a7ee995cda6679b14d43d26 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 13 Sep 2016 10:27:06 +0200 Subject: [PATCH 473/701] Python library for Google protobuf, compiled using foss 2016a. --- ...f-python-3.0.2-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ ...uf-python-3.0.2-foss-2016a-Python-3.5.1.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1ff4a4ad43 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.0.2' +versionsuffix= '-Python-%(version)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +versionsuffix = '-Python-%(pyver)s' + +dependencies = [ + ('Python', '2.7.11'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/protobuf-%(version)s-py%(pyshortver)s.egg/google/__init__.py'], + 'dirs': ['bin'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..2c3f2283d9 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.0.2' +versionsuffix= '-Python-%(version)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +versionsuffix = '-Python-%(pyver)s' + +dependencies = [ + ('Python', '3.5.1'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/protobuf-%(version)s-py%(pyshortver)s.egg/google/__init__.py'], + 'dirs': ['bin'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' -- GitLab From 8887b51468d87ad0d3db90d9af09bc8a9e221bf4 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 13 Sep 2016 16:18:21 +0200 Subject: [PATCH 474/701] newer expat version in dbus-glib --- easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb index 3a355efc71..8d6e6a7449 100644 --- a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('GLib', '2.48.0'), ('DBus', '1.10.8'), - ('expat', '2.2.0'), + ('expat', '2.2.1'), ] sanity_check_paths = { -- GitLab From 3911624c610e3d3921fccb114d737f7f560479c8 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 13 Sep 2016 16:21:55 +0200 Subject: [PATCH 475/701] older 2.1.1 version instead of non existing newer --- easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb index 8d6e6a7449..3d05e04fc1 100644 --- a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.106-foss-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('GLib', '2.48.0'), ('DBus', '1.10.8'), - ('expat', '2.2.1'), + ('expat', '2.1.1'), ] sanity_check_paths = { -- GitLab From 26d4b8d3d274a0fe57498fa2650b34f96ee87660 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 13 Sep 2016 16:29:09 +0200 Subject: [PATCH 476/701] Fixed: - versionsuffix - removed check for __init__.py in egg directory - check for site-packages directory instead - removed check for bin directory as it does not contain important files --- .../protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb | 8 +++----- .../protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb | 8 +++----- 2 files changed, 6 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb index 1ff4a4ad43..3deb45334a 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.0.2' -versionsuffix= '-Python-%(version)s' +versionsuffix= '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" @@ -12,8 +12,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] sources = [SOURCE_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' - dependencies = [ ('Python', '2.7.11'), ('protobuf', version) @@ -22,8 +20,8 @@ dependencies = [ start_dir = 'python' sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/protobuf-%(version)s-py%(pyshortver)s.egg/google/__init__.py'], - 'dirs': ['bin'], + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } options = {'modulename': 'google.protobuf' } diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb index 2c3f2283d9..64b04ec53c 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.0.2' -versionsuffix= '-Python-%(version)s' +versionsuffix= '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" @@ -12,8 +12,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] sources = [SOURCE_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' - dependencies = [ ('Python', '3.5.1'), ('protobuf', version) @@ -22,8 +20,8 @@ dependencies = [ start_dir = 'python' sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/protobuf-%(version)s-py%(pyshortver)s.egg/google/__init__.py'], - 'dirs': ['bin'], + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } options = {'modulename': 'google.protobuf' } -- GitLab From 32be622670f9044a07e531796b7a8e8cdce4f2f6 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 14 Sep 2016 11:26:05 +0200 Subject: [PATCH 477/701] Bison builddep included --- .../g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb index 7583a907a1..3bfa7c6721 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -22,6 +22,7 @@ dependencies = [ builddependencies = [ ('Autotools', '20150215'), ('pkg-config', '1.1.0', '-Python-2.7.11'), + ('Bison', '3.0.4', '', True), ] sanity_check_paths = { -- GitLab From 4f24f16c0115796da48f91f2e3e6e63071c940ae Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 14 Sep 2016 11:29:36 +0200 Subject: [PATCH 478/701] pkgconfig version --- .../g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb index 3bfa7c6721..293e76a477 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -21,7 +21,7 @@ dependencies = [ builddependencies = [ ('Autotools', '20150215'), - ('pkg-config', '1.1.0', '-Python-2.7.11'), + ('pkg-config', '0.29.1', '-Python-2.7.11'), ('Bison', '3.0.4', '', True), ] -- GitLab From 31f72e28d48156c5846e0ffa2cd2b12597674ef8 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 14 Sep 2016 11:54:01 +0200 Subject: [PATCH 479/701] out of the woods? --- .../g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb index 293e76a477..248204c8cc 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -21,7 +21,7 @@ dependencies = [ builddependencies = [ ('Autotools', '20150215'), - ('pkg-config', '0.29.1', '-Python-2.7.11'), + ('pkg-config', '0.29.1'), ('Bison', '3.0.4', '', True), ] @@ -36,4 +36,4 @@ modextrapaths = { 'XDG_DATA_DIRS': 'share', } -moduleclass = 'vis' \ No newline at end of file +moduleclass = 'vis' -- GitLab From 9b526284b4915166290aa17aac570220cc56ac3e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 14 Sep 2016 12:51:56 +0200 Subject: [PATCH 480/701] verifyBamID with foss2016a --- .../verifyBamID-1.1.3-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000..0eaa48f9c3 --- /dev/null +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'verifyBamID' +version = '1.1.3' + +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. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/statgen/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)sLibStatGen.%(version)s.tgz'] + +checksums = ['9b3d4c73c8f72e6b8f1e014702bc5bec'] + +executables = ['%(name)s/bin/%(name)s'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 11594910285f4f06bc92fcdd9968bb49df6961fa Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 16:32:15 +0200 Subject: [PATCH 481/701] add easyconfig bwakit-0.7.15_x64-linux.eb --- .../b/bwakit/bwakit-0.7.15_x64-linux.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb diff --git a/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb new file mode 100644 index 0000000000..fe095b5c13 --- /dev/null +++ b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'bwakit' +version = '0.7.15' +versionsuffix = '_x64-linux' + +homepage = 'https://github.com/lh3/bwa/tree/master/bwakit' +description = """Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://sourceforge.net/projects/bio-bwa/files/bwakit/'] +sources = ['%(name)s-%(version)s%(versionsuffix)s.tar.bz2'] + +sanity_check_paths = { + 'files': ['bwa', 'samtools'], + 'dirs': [] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", +} + +moduleclass = 'bio' -- GitLab From 2037a1c7e6eda0d3e6456b834ac958a094d4cf42 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Wed, 14 Sep 2016 16:45:34 +0200 Subject: [PATCH 482/701] style fix --- easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb index fe095b5c13..5e016d4b0d 100644 --- a/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb +++ b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb @@ -10,7 +10,8 @@ version = '0.7.15' versionsuffix = '_x64-linux' homepage = 'https://github.com/lh3/bwa/tree/master/bwakit' -description = """Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.""" +description = """Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, +providing an end-to-end solution to read mapping.""" toolchain = {'name': 'dummy', 'version': ''} -- GitLab From ddc39bfa7c5c233c737683632eae8122b77a181c Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 14 Sep 2016 16:56:15 +0200 Subject: [PATCH 483/701] new version of jmodeltest --- ....1.10r20160303-foss-2016a-Java-1.8.0_92.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb new file mode 100644 index 0000000000..242bfeb229 --- /dev/null +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PackedBinary' + +name = 'jModelTest' +version = '2.1.10r20160303' + +homepage = 'https://github.com/ddarriba/jmodeltest2' +description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/ddarriba/jmodeltest2/archive/'] +sources = ['v%(version)s.tar.gz'] + +java = 'Java' +javaver = '1.8.0_92' +versionsuffix = '-%s-%s' % (java, javaver) + +builddependencies = [('ant', '1.9.7', '%(versionsuffix)s', True)] + +dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] + +install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" + +modloadmsg = """To execute jModelTest run: java -jar \\$EBROOTJMODELTEST/jModelTest.jar""" + +sanity_check_paths = { + 'files': ['jModelTest.jar'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 51b37d5dc5bfac276311c27b34f7dd7ceba91460 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 14 Sep 2016 16:56:49 +0200 Subject: [PATCH 484/701] updated dependencies of mpj express, which itself is a dependency of jmodeltest --- ...J-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb new file mode 100644 index 0000000000..4d87ddfc86 --- /dev/null +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'MPJ-Express' +version = '0.44' + +homepage = 'http://mpj-express.org/' +description = """MPJ Express is an open source Java message passing library that allows application + developers to write and execute parallel applications for multicore processors and compute clusters/clouds.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://sourceforge.net/projects/mpjexpress/files/releases/'] +sources = ['mpj-v%s.tar.gz' % (version.replace('.','_'))] + +java = 'Java' +javaver = '1.8.0_92' +versionsuffix = '-%s-%s' % (java, javaver) + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + (java, javaver, '', True), +] + +# compile JNI wrapper library as described in docs +# http://mpj-express.org/docs/readme/README +postinstallcmds = ["mkdir %(installdir)s/src/mpjdev/natmpjdev/lib/build", + "cd %(installdir)s/src/mpjdev/natmpjdev/lib/build && cmake .. && make && make install DESTDIR=%(installdir)s",] + +modextrapaths = { + 'CLASSPATH': 'lib', +} + +modextravars = { + 'MPJ_HOME': '$root', # MPJ_HOME points to install directory +} + +sanity_check_paths = { + 'files': ['lib/libnativempjdev.so', 'bin/mpjrun.sh'], + 'dirs': [] +} + +moduleclass = 'lib' -- GitLab From 4c3e6fbdd1d319376bae69e7ab43ffb24048bcd6 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 14 Sep 2016 17:19:12 +0200 Subject: [PATCH 485/701] CXX in buildopts --- .../easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb index 0eaa48f9c3..d08f6ddb12 100644 --- a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb @@ -17,6 +17,8 @@ sources = ['%(name)sLibStatGen.%(version)s.tgz'] checksums = ['9b3d4c73c8f72e6b8f1e014702bc5bec'] +buildopts = 'CXX="$CXX"' + executables = ['%(name)s/bin/%(name)s'] files_to_copy = [(executables, 'bin')] -- GitLab From 3fa53e040d002e21d96536b3342c931900fe5cff Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 14 Sep 2016 17:25:49 +0200 Subject: [PATCH 486/701] expat and GST version --- .../w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb index abb19d3368..a3cb9a333d 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb @@ -21,10 +21,10 @@ dependencies = [ ('zlib', '1.2.8'), ('libjpeg-turbo', '1.5.0'), ('LibTIFF', '4.0.6'), - ('expat', '2.2.0'), + ('expat', '2.1.1'), ('GTK+', '2.24.30'), ('GConf', '3.2.6'), - ('GST-plugins-base', '1.9.1'), + ('GST-plugins-base', '1.8.3'), ('libGLU', '9.0.0', '-Mesa-11.2.1'), ('libSM', '1.2.2'), ('libXxf86vm', '1.1.4'), -- GitLab From 6c0009557bd08a17e1c85d7cac7e4d98cce8b0dc Mon Sep 17 00:00:00 2001 From: Bob Date: Thu, 15 Sep 2016 10:11:55 +0200 Subject: [PATCH 487/701] Foss toolchain is not needed, just Java is enough --- ...est-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb index 242bfeb229..00bc8cb97d 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb @@ -7,22 +7,22 @@ easyblock = 'PackedBinary' name = 'jModelTest' version = '2.1.10r20160303' +versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/ddarriba/jmodeltest2' description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" -toolchain = {'name': 'foss', 'version': '2016a'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/ddarriba/jmodeltest2/archive/'] sources = ['v%(version)s.tar.gz'] -java = 'Java' -javaver = '1.8.0_92' -versionsuffix = '-%s-%s' % (java, javaver) +builddependencies = [('ant', '1.9.7', versionsuffix)] -builddependencies = [('ant', '1.9.7', '%(versionsuffix)s', True)] - -dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] +dependencies = [ + ('MPJ-Express', '0.44', versionsuffix, ('foss', '2016a')), + ('Java', '1.8.0_92'), +] install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" -- GitLab From 6751da8d5a315b688fbac871d97291134666358b Mon Sep 17 00:00:00 2001 From: Bob Date: Thu, 15 Sep 2016 10:12:39 +0200 Subject: [PATCH 488/701] Remove foss from filename --- ...ModelTest-2.1.10r20160303-Java-1.8.0_92.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb new file mode 100644 index 0000000000..00bc8cb97d --- /dev/null +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PackedBinary' + +name = 'jModelTest' +version = '2.1.10r20160303' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/ddarriba/jmodeltest2' +description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/ddarriba/jmodeltest2/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('ant', '1.9.7', versionsuffix)] + +dependencies = [ + ('MPJ-Express', '0.44', versionsuffix, ('foss', '2016a')), + ('Java', '1.8.0_92'), +] + +install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" + +modloadmsg = """To execute jModelTest run: java -jar \\$EBROOTJMODELTEST/jModelTest.jar""" + +sanity_check_paths = { + 'files': ['jModelTest.jar'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From f3269b12f1e5c882a24230eea42cf675f21d7038 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 15 Sep 2016 10:13:19 +0200 Subject: [PATCH 489/701] Delete jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb --- ....1.10r20160303-foss-2016a-Java-1.8.0_92.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb deleted file mode 100644 index 00bc8cb97d..0000000000 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-foss-2016a-Java-1.8.0_92.eb +++ /dev/null @@ -1,36 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'PackedBinary' - -name = 'jModelTest' -version = '2.1.10r20160303' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://github.com/ddarriba/jmodeltest2' -description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" - -toolchain = {'name': 'dummy', 'version': ''} - -source_urls = ['https://github.com/ddarriba/jmodeltest2/archive/'] -sources = ['v%(version)s.tar.gz'] - -builddependencies = [('ant', '1.9.7', versionsuffix)] - -dependencies = [ - ('MPJ-Express', '0.44', versionsuffix, ('foss', '2016a')), - ('Java', '1.8.0_92'), -] - -install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" - -modloadmsg = """To execute jModelTest run: java -jar \\$EBROOTJMODELTEST/jModelTest.jar""" - -sanity_check_paths = { - 'files': ['jModelTest.jar'], - 'dirs': [], -} - -moduleclass = 'bio' -- GitLab From eefa47e87cde84b64b3dd591f33c4e060abdbab0 Mon Sep 17 00:00:00 2001 From: Bob Date: Thu, 15 Sep 2016 10:23:12 +0200 Subject: [PATCH 490/701] small change in position of versionsuffix, use javaver --- .../MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index 4d87ddfc86..0a8633bccd 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -7,6 +7,7 @@ easyblock = 'Tarball' name = 'MPJ-Express' version = '0.44' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://mpj-express.org/' description = """MPJ Express is an open source Java message passing library that allows application @@ -17,14 +18,10 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourceforge.net/projects/mpjexpress/files/releases/'] sources = ['mpj-v%s.tar.gz' % (version.replace('.','_'))] -java = 'Java' -javaver = '1.8.0_92' -versionsuffix = '-%s-%s' % (java, javaver) - builddependencies = [('CMake', '3.5.2')] dependencies = [ - (java, javaver, '', True), + ('Java', '1.8.0_92', '', True), ] # compile JNI wrapper library as described in docs -- GitLab From 4c71115eb1c0521c2a3161e16bb39e766d3e13f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Sep 2016 12:51:56 +0200 Subject: [PATCH 491/701] add easyconfig f90cache-0.96.eb --- .../easyconfigs/f/f90cache/f90cache-0.96.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb diff --git a/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb b/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb new file mode 100644 index 0000000000..e0fc7d99c5 --- /dev/null +++ b/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'f90cache' +version = '0.96' + +homepage = 'http://people.irisa.fr/Edouard.Canot/f90cache/' +description = """f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, + using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. + This often results in a great speedup in common compilations.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://people.irisa.fr/Edouard.Canot/f90cache/'] +sources = [SOURCE_TAR_BZ2] + +buildopts = "CFLAGS='-O2 -static'" + +sanity_check_paths = { + 'files': ['bin/f90cache'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 82cbc6360716b59b068cee31dde49e517d18b0fc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 15 Sep 2016 12:53:19 +0100 Subject: [PATCH 492/701] add easyconfig Boost-1.61.0-foss-2016b.eb, add easyconfig GROMACS-5.1.4-foss-2016b-hybrid.eb, add easyconfig GROMACS-5.1.4-foss-2016b-mt.eb --- .../b/Boost/Boost-1.61.0-foss-2016b.eb | 23 +++++++++++ .../GROMACS-5.1.4-foss-2016b-hybrid.eb | 39 +++++++++++++++++++ .../g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb | 39 +++++++++++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016b.eb new file mode 100644 index 0000000000..876bfa42e6 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016b.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.61.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +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' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb new file mode 100644 index 0000000000..2e153e4c27 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.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 / 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 +# +# Version 5.1.4 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.4' +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': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('libxml2', '2.9.4') +] + +dependencies = [('Boost', '1.61.0')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb new file mode 100644 index 0000000000..ab660ee955 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.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 / 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 +# +# Version 5.1.4 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.4' +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': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('libxml2', '2.9.4') +] + +dependencies = [('Boost', '1.61.0')] + +moduleclass = 'bio' -- GitLab From f51c1bfa1f736922e15040975adafa9f7b6ce1b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Sep 2016 14:02:31 +0200 Subject: [PATCH 493/701] add easyconfig ccache-3.3.1.eb --- .../easyconfigs/c/ccache/ccache-3.3.1.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb b/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb new file mode 100644 index 0000000000..66a9fe225a --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb @@ -0,0 +1,36 @@ +## +# 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 +# $Id$ +## +easyblock = 'ConfigureMake' + +name = 'ccache' +version = '3.3.1' + +homepage = 'http://ccache.samba.org/' +description = """ccache-3.1.9: Cache for C/C++ compilers""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'static': True} + +source_urls = ['https://github.com/ccache/ccache/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('Autotools', '20150215'), + ('zlib', '1.2.8'), +] + +preconfigopts = "./autogen.sh && " +buildopts = 'LDFLAGS="-static"' + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From d4b6f3bcb621cdb68fcdde6efb70754b7f21c37f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 15 Sep 2016 16:18:28 +0200 Subject: [PATCH 494/701] resolve dep conflicts --- .../w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb index a3cb9a333d..0e8d3f9d34 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', '2.7.11'), ('libpng', '1.6.21'), ('zlib', '1.2.8'), - ('libjpeg-turbo', '1.5.0'), + ('libjpeg-turbo', '1.4.2'), ('LibTIFF', '4.0.6'), ('expat', '2.1.1'), ('GTK+', '2.24.30'), -- GitLab From 9fee61323514bdbe0dc8792da18538ab70e7b60e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 16 Sep 2016 10:15:34 +0200 Subject: [PATCH 495/701] OBITools with foss2016a --- .../Cython-0.23.5-foss-2016a-Python-2.7.11.eb | 24 +++++++++++++ .../Cython-0.24-foss-2016a-Python-2.7.11.eb | 24 +++++++++++++ .../Cython-0.24.1-foss-2016a-Python-2.7.11.eb | 24 +++++++++++++ ...OBITools-1.2.6-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ ...OBITools-1.2.9-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 5 files changed, 140 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.23.5-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.24-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/o/OBITools/OBITools-1.2.6-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.23.5-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cython/Cython-0.23.5-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..51de06bbef --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.23.5-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.23.5' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg' +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': [cythonlibdir + '/%(name)s'] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.24-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cython/Cython-0.24-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a9134a498b --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.24-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.24' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg' +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': [cythonlibdir + '/%(name)s'] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a2db0bddbe --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.24.1' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg' +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': [cythonlibdir + '/%(name)s'] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.6-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.6-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..cd5245c6e2 --- /dev/null +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.6-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'OBITools' +version = '1.2.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.grenoble.prabi.fr/trac/OBITools' +description = """ The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using + the Unix command line interface. They follow the standard Unix interface for command line program, allowing to chain a set of + commands using the pipe mecanism. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + + +dependencies = [ + ('Python', '2.7.11'), + ('Cython', '0.23.5', versionsuffix), # Has to be 0.23.5 + ('wheel', '0.29.0', versionsuffix), + ('IPython', '5.0.0', versionsuffix), + ('Sphinx', '1.4.5', versionsuffix) +] + +options = {'modulename': 'obitools'} + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ['ali2consensus','ecotag','obiaddtaxids','obicount','obistat']], + 'dirs': ['bin','lib/python%(pyshortver)s/site-packages/obitools'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..8ecf00679f --- /dev/null +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'OBITools' +version = '1.2.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.grenoble.prabi.fr/trac/OBITools' +description = """ The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using + the Unix command line interface. They follow the standard Unix interface for command line program, allowing to chain a set of + commands using the pipe mecanism. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + + +dependencies = [ + ('Python', '2.7.11'), + ('Cython', '0.24.1', versionsuffix), + ('wheel', '0.29.0', versionsuffix), + ('IPython', '5.0.0', versionsuffix), + ('Sphinx', '1.4.5', versionsuffix) +] + +options = {'modulename': 'obitools'} + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ['ali2consensus','ecotag','obiaddtaxids','obicount','obistat']], + 'dirs': ['bin','lib/python%(pyshortver)s/site-packages/obitools'], +} + +moduleclass = 'math' -- GitLab From cd36f5dfc0f5b18cf614075ed15e2825de029229 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 16 Sep 2016 10:16:40 +0200 Subject: [PATCH 496/701] remove older version files --- .../Cython-0.23.5-foss-2016a-Python-2.7.11.eb | 24 ------------- .../Cython-0.24-foss-2016a-Python-2.7.11.eb | 24 ------------- ...OBITools-1.2.6-foss-2016a-Python-2.7.11.eb | 34 ------------------- 3 files changed, 82 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.23.5-foss-2016a-Python-2.7.11.eb delete mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.24-foss-2016a-Python-2.7.11.eb delete mode 100644 easybuild/easyconfigs/o/OBITools/OBITools-1.2.6-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.23.5-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cython/Cython-0.23.5-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index 51de06bbef..0000000000 --- a/easybuild/easyconfigs/c/Cython/Cython-0.23.5-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Cython' -version = '0.23.5' -versionsuffix = '-Python-%(pyver)s' - -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.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [('Python', '2.7.11')] - -cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg' -sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], - 'dirs': [cythonlibdir + '/%(name)s'] -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.24-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cython/Cython-0.24-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index a9134a498b..0000000000 --- a/easybuild/easyconfigs/c/Cython/Cython-0.24-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Cython' -version = '0.24' -versionsuffix = '-Python-%(pyver)s' - -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.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [('Python', '2.7.11')] - -cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg' -sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], - 'dirs': [cythonlibdir + '/%(name)s'] -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.6-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.6-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index cd5245c6e2..0000000000 --- a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.6-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = "PythonPackage" - -name = 'OBITools' -version = '1.2.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.grenoble.prabi.fr/trac/OBITools' -description = """ The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using - the Unix command line interface. They follow the standard Unix interface for command line program, allowing to chain a set of - commands using the pipe mecanism. -""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - - -dependencies = [ - ('Python', '2.7.11'), - ('Cython', '0.23.5', versionsuffix), # Has to be 0.23.5 - ('wheel', '0.29.0', versionsuffix), - ('IPython', '5.0.0', versionsuffix), - ('Sphinx', '1.4.5', versionsuffix) -] - -options = {'modulename': 'obitools'} - -sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ['ali2consensus','ecotag','obiaddtaxids','obicount','obistat']], - 'dirs': ['bin','lib/python%(pyshortver)s/site-packages/obitools'], -} - -moduleclass = 'math' -- GitLab From f7fb8f535fe43730b3dd8a2ce2372bddc6a1a33e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 16 Sep 2016 10:19:12 +0200 Subject: [PATCH 497/701] GStreamer and GST-plugins-base 0.10 versions --- .../GST-plugins-base-0.10.36-foss-2016a.eb | 35 ++++++++++++++++ .../GStreamer/GStreamer-0.10.36-foss-2016a.eb | 40 +++++++++++++++++++ ...Python-3.0.2.0-foss-2016a-Python-2.7.11.eb | 4 +- 3 files changed, 77 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb new file mode 100644 index 0000000000..d0bab44734 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) 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-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb new file mode 100644 index 0000000000..3dddb7ed20 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +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': 'foss', 'version': '2016a'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.48.0'), + ('GObject-Introspection', '1.48.0'), + ('zlib', '1.2.8'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) 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/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb index 0e8d3f9d34..ddb87ab0aa 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2016a-Python-2.7.11.eb @@ -19,12 +19,12 @@ dependencies = [ ('Python', '2.7.11'), ('libpng', '1.6.21'), ('zlib', '1.2.8'), - ('libjpeg-turbo', '1.4.2'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), ('LibTIFF', '4.0.6'), ('expat', '2.1.1'), ('GTK+', '2.24.30'), ('GConf', '3.2.6'), - ('GST-plugins-base', '1.8.3'), + ('GST-plugins-base', '0.10.36'), ('libGLU', '9.0.0', '-Mesa-11.2.1'), ('libSM', '1.2.2'), ('libXxf86vm', '1.1.4'), -- GitLab From 6f64c98d078beb5de89e99519729587d742c7895 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 16 Sep 2016 12:42:44 +0200 Subject: [PATCH 498/701] Log-Log4perl foss2016a --- .../Log-Log4perl-1.47-foss-2016a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/Log-Log4perl/Log-Log4perl-1.47-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/Log-Log4perl/Log-Log4perl-1.47-foss-2016a.eb b/easybuild/easyconfigs/l/Log-Log4perl/Log-Log4perl-1.47-foss-2016a.eb new file mode 100644 index 0000000000..da1c7223b7 --- /dev/null +++ b/easybuild/easyconfigs/l/Log-Log4perl/Log-Log4perl-1.47-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'PerlModule' + +name = 'Log-Log4perl' +version = '1.47' + +homepage = 'https://metacpan.org/pod/Log::Log4perl' +description = """Log4perl""" + +toolchain = {'name': 'foss', 'version': '2016a'} +source_urls = ['https://cpan.metacpan.org/authors/id/M/MS/MSCHILLI/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.22.1' +perlversuffix = '-bare' + +dependencies = [ + (perl, perlver, perlversuffix) +] + +options = {'modulename': 'Log::Log4perl'} + +moduleclass = 'data' -- GitLab From aa2c671f7747b10eb7ad153206b8488c174d84a9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 11:26:26 +0200 Subject: [PATCH 499/701] Cairo for intel/2016b --- .../c/cairo/cairo-1.14.6-intel-2016b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb new file mode 100644 index 0000000000..8b72c69a68 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +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': '2016b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('freetype', '2.6.5'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('X11', '20160819'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 5e8ddb02cb38f9cb339d243d8f1d198fce69d8cc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 11:36:52 +0200 Subject: [PATCH 500/701] Pango/1.40.3 for intel/2016b --- ...Object-Introspection-1.49.2-intel-2016b.eb | 47 +++++++++++++++++++ .../h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb | 34 ++++++++++++++ .../p/Pango/Pango-1.40.3-intel-2016b.eb | 31 ++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.2-intel-2016b.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.2-intel-2016b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.2-intel-2016b.eb new file mode 100644 index 0000000000..616a0c8d65 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.2-intel-2016b.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.49.2' + +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': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.12'), + ('GLib', '2.49.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +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'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb new file mode 100644 index 0000000000..7471de5f95 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.3.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GLib', '2.49.5'), + ('cairo', '1.14.6'), + ('freetype', '2.6.5'), +] + +builddependencies = [('GObject-Introspection', '1.49.2')] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb new file mode 100644 index 0000000000..f3c71a9da5 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.3' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('X11', '20160819'), + ('GLib', '2.49.5'), + ('cairo', '1.14.6'), + ('HarfBuzz', '1.3.1'), +] + +builddependencies = [('GObject-Introspection', '1.49.2')] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From 796ac5ce7b709eae33faf21df1ec77939d47bda0 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 12:01:51 +0200 Subject: [PATCH 501/701] Add pixman/0.34.0 for intel/2016b --- .../p/pixman/pixman-0.34.0-intel-2016b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb new file mode 100644 index 0000000000..ae4b777250 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +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': '2016b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 1b6a3b94b79fff5e9429b6f994ec0d2ffa96dbb4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 19 Sep 2016 13:57:04 +0200 Subject: [PATCH 502/701] add easyconfig Java-1.6.0_24.eb --- easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb b/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb new file mode 100644 index 0000000000..c6a48a76b4 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb @@ -0,0 +1,42 @@ +# Built with EasyBuild version 2.8.0 on 2016-06-01_16-05-57 +name = 'Java' +version = '1.6.0_24' + +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.bin' % altver] + +moduleclass = 'lang' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.8.0", + "easybuild-easyblocks_version": "2.8.0", + "timestamp": 1464789948, + "build_time": 96.02, + "install_size": 229623303, + "command_line": ['--buildpath=/export/soft/easybuild/build-dir/generic', '--configfiles=/scicore/soft/apps/easybuild-config-files/generic.cfg', '--filter-deps=GLib,libX11,libXt,libXrender', '--force', '--hide-deps=ncurses,zlib,bzip2,libpng,libreadline,libjpeg-turbo,libxml2,libxslt,Tk,Tcl,LibTIFF,OpenSSL,cairo,expat,gettext,pixman,fontconfig', '--include-easyblocks=java.py', '--installpath=/scicore/soft', '--modules-tool=Lmod', '--optarch=GENERIC', '--package', '--packagepath=/export/soft/RPMs/centos6/generic/', '--repository=GitRepository', '--repositorypath=git@bc2-gl.bc2.unibas.ch:easybuild/installed_easyconfigs.git,generic', '--sourcepath=/export/soft/source', '--subdir-software=apps', '--tmp-logdir=/export/soft/easybuild/build-dir/generic', '--tmpdir=/export/soft/easybuild/build-dir/generic', '--umask=022', 'Java-1.6.0_24.eb'], + "modules_tool": ('Lmod', '/export/soft/lua_lmod/centos6/lmod/lmod/libexec/lmod', '6.0.9'), + "core_count": 8, + "cpu_model": "Intel(R) Xeon(R) CPU E5620 @ 2.40GHz", + "cpu_speed": 2394.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; Target: x86_64-redhat-linux; Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux; Thread model: posix; gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC) ; ", + "glibc_version": "2.12", + "hostname": "login18.cluster.bc2.ch", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.5", + "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": "/usr/bin/gcc", + "system_python_path": "/usr/bin/python", + "total_memory": 48255, +}] -- GitLab From 632775ca42624540faa90acf3b914046af414799 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Mon, 19 Sep 2016 13:57:43 +0200 Subject: [PATCH 503/701] removed build statistics --- easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb | 27 ------------------- 1 file changed, 27 deletions(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb b/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb index c6a48a76b4..ec1642238f 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.8.0 on 2016-06-01_16-05-57 name = 'Java' version = '1.6.0_24' @@ -14,29 +13,3 @@ altver = '%su%s' % (vp.split('.')[1], vs) sources = ['jdk-%s-linux-x64.bin' % altver] moduleclass = 'lang' - -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.8.0", - "easybuild-easyblocks_version": "2.8.0", - "timestamp": 1464789948, - "build_time": 96.02, - "install_size": 229623303, - "command_line": ['--buildpath=/export/soft/easybuild/build-dir/generic', '--configfiles=/scicore/soft/apps/easybuild-config-files/generic.cfg', '--filter-deps=GLib,libX11,libXt,libXrender', '--force', '--hide-deps=ncurses,zlib,bzip2,libpng,libreadline,libjpeg-turbo,libxml2,libxslt,Tk,Tcl,LibTIFF,OpenSSL,cairo,expat,gettext,pixman,fontconfig', '--include-easyblocks=java.py', '--installpath=/scicore/soft', '--modules-tool=Lmod', '--optarch=GENERIC', '--package', '--packagepath=/export/soft/RPMs/centos6/generic/', '--repository=GitRepository', '--repositorypath=git@bc2-gl.bc2.unibas.ch:easybuild/installed_easyconfigs.git,generic', '--sourcepath=/export/soft/source', '--subdir-software=apps', '--tmp-logdir=/export/soft/easybuild/build-dir/generic', '--tmpdir=/export/soft/easybuild/build-dir/generic', '--umask=022', 'Java-1.6.0_24.eb'], - "modules_tool": ('Lmod', '/export/soft/lua_lmod/centos6/lmod/lmod/libexec/lmod', '6.0.9'), - "core_count": 8, - "cpu_model": "Intel(R) Xeon(R) CPU E5620 @ 2.40GHz", - "cpu_speed": 2394.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; Target: x86_64-redhat-linux; Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux; Thread model: posix; gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC) ; ", - "glibc_version": "2.12", - "hostname": "login18.cluster.bc2.ch", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.5", - "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": "/usr/bin/gcc", - "system_python_path": "/usr/bin/python", - "total_memory": 48255, -}] -- GitLab From f0a42c7edd985a11ee0ae5037e75758d01450452 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 14:02:03 +0200 Subject: [PATCH 504/701] Add SWIG/3.0.8 for Python/3.5.2 and intel/2016b --- .../SWIG-3.0.8-intel-2016b-Python-3.5.2.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..230fa8885d --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.8' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' -- GitLab From efe52a5a9cfbefcca561ba49680950ced58cbb07 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 14:04:16 +0200 Subject: [PATCH 505/701] Drop to 1.49.1 for GObject-Introspection (else needs newer glib) --- easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb | 2 +- ...tel-2016b.eb => GObject-Introspection-1.49.1-intel-2016b.eb} | 2 +- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/g/GObject-Introspection/{GObject-Introspection-1.49.2-intel-2016b.eb => GObject-Introspection-1.49.1-intel-2016b.eb} (98%) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb index 8b72c69a68..54967b2ef7 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb @@ -25,7 +25,7 @@ dependencies = [ ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes " +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " # workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.2-intel-2016b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-intel-2016b.eb similarity index 98% rename from easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.2-intel-2016b.eb rename to easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-intel-2016b.eb index 616a0c8d65..09a8cb39dc 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.2-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-intel-2016b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GObject-Introspection' -version = '1.49.2' +version = '1.49.1' homepage = 'https://wiki.gnome.org/GObjectIntrospection/' description = """GObject introspection is a middleware layer between C libraries diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb index 7471de5f95..6a9022cf44 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2016b.eb @@ -17,7 +17,7 @@ dependencies = [ ('freetype', '2.6.5'), ] -builddependencies = [('GObject-Introspection', '1.49.2')] +builddependencies = [('GObject-Introspection', '1.49.1')] configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb index f3c71a9da5..16a2426440 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('HarfBuzz', '1.3.1'), ] -builddependencies = [('GObject-Introspection', '1.49.2')] +builddependencies = [('GObject-Introspection', '1.49.1')] configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " -- GitLab From 5f837e79f20ca7913b78ef57635998934aaa05ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Sep 2016 14:04:44 +0200 Subject: [PATCH 506/701] enable running of tests for HPCG --- easybuild/easyconfigs/h/HPCG/HPCG-2.1-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/h/HPCG/HPCG-2.1-ictce-5.5.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCG/HPCG-2.1-goolf-1.4.10.eb index 06eaeceafd..cc1b322548 100644 --- a/easybuild/easyconfigs/h/HPCG/HPCG-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCG/HPCG-2.1-goolf-1.4.10.eb @@ -11,4 +11,6 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['https://software.sandia.gov/hpcg/downloads/'] sources = [SOURCELOWER_TAR_GZ] +runtest = True + moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-2.1-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HPCG/HPCG-2.1-ictce-5.5.0.eb index 1d3f7c2d89..550fcae2be 100644 --- a/easybuild/easyconfigs/h/HPCG/HPCG-2.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/HPCG/HPCG-2.1-ictce-5.5.0.eb @@ -11,4 +11,6 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['https://software.sandia.gov/hpcg/downloads/'] sources = [SOURCELOWER_TAR_GZ] +runtest = True + moduleclass = 'math' -- GitLab From 1cb97141ef181fd294856dd68ded77d3d93742ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Sep 2016 14:06:36 +0200 Subject: [PATCH 507/701] remove --with-tcl-config/--with-tk-config from R easyconfig, already done in R easyblock --- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 5a44f1a48c..1a886a00c9 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -15,8 +15,6 @@ 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=yes --enable-R-shlib" -#Actually use Tcl/Tk -configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' # Enable graphics capabilities for plotting. configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" # some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below -- GitLab From 77245218a97521b5c5f12260d2f73c463257d607 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 14:50:42 +0200 Subject: [PATCH 508/701] Added Theano/0.8.2 for intel/2016b + Python 3.5.2 Would pydot for visualization --- .../Theano-0.8.2-intel-2016b-Python-3.5.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..c94eb7afed --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +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': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +builddependencies = [('nose-parameterized', '0.5.0', versionsuffix)] + +runtests = 'nosetests theano' + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'math' -- GitLab From ff342324c7dceb2f22ce786e9da40fa3a4e89d1a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 14:53:08 +0200 Subject: [PATCH 509/701] Add forgotten dep: nose-parameterized --- ...eterized-0.5.0-intel-2016b-Python-3.5.2.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..be6e199cd9 --- /dev/null +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'nose-parameterized' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'hmat://github.com/wolever/nose-parameterized' +description = """Parameterized testing with any Python test framework.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +options = {'modulename': 'nose_parameterized'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nose_parameterized-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' -- GitLab From 012d39f1acccea70bdc9cc74577140cfaaa32127 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 14:59:57 +0200 Subject: [PATCH 510/701] h5py for Python/3.5.2+intel/2016b+HDF5/1.8.17 --- ....0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb | 34 +++++++++++++++++++ ...kgconfig-1.1.0-intel-2016b-Python-3.5.2.eb | 26 ++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb new file mode 100644 index 0000000000..156acadec8 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.17.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.6.0' + +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': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.17' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.5.2'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..2723e2f049 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('pkg-config', '0.29.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From 6ab4c08ef47d3c0d4f3bfad5bfbbc9449d05a191 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 15:01:04 +0200 Subject: [PATCH 511/701] Add Keras/1.0.8 --- .../Keras-1.0.8-intel-2016b-Python-3.5.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..5d47272ae6 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'Keras' +version = '1.0.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('Theano', '0.8.2', versionsuffix), + ('h5py', '2.6.0', '%(versionsuffix)s-HDF5-1.8.17'), +] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'math' -- GitLab From a9721ecefb40917b2afdf8f95209aa0d14d252bf Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 15:02:06 +0200 Subject: [PATCH 512/701] Fix typo in Theano --- .../t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb index c94eb7afed..55c8d13a89 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb @@ -17,7 +17,7 @@ dependencies = [('Python', '3.5.2')] builddependencies = [('nose-parameterized', '0.5.0', versionsuffix)] -runtests = 'nosetests theano' +runtest = 'nosetests theano' sanity_check_paths = { 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], -- GitLab From b17d614ac96aa042fd3325e9deaaf535cd2bbb2a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 15:52:05 +0200 Subject: [PATCH 513/701] Add PyYAML to Keras --- .../k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb index 5d47272ae6..76540365f0 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb @@ -17,10 +17,11 @@ dependencies = [ ('Python', '3.5.2'), ('Theano', '0.8.2', versionsuffix), ('h5py', '2.6.0', '%(versionsuffix)s-HDF5-1.8.17'), + ('PyYAML', '3.12', versionsuffix), ] sanity_check_paths = { - 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], + 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], } -- GitLab From b233043902c2fc214d7975d7a2090050ccd75846 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 15:52:57 +0200 Subject: [PATCH 514/701] Add PyYAML easyconfig --- .../PyYAML-3.12-intel-2016b-Python-3.5.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..5e2dea3692 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +pyver = '3.5.2' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Python', pyver), + ('libyaml', '0.1.6'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/yaml' % pyshortver], +} + +moduleclass = 'lib' -- GitLab From 96eb5e530cedbcaa8d0d576fa2d3394da189b8db Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 17:06:24 +0200 Subject: [PATCH 515/701] Drop tests (takes too long) --- .../t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb index 55c8d13a89..fdea58014e 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-intel-2016b-Python-3.5.2.eb @@ -17,11 +17,12 @@ dependencies = [('Python', '3.5.2')] builddependencies = [('nose-parameterized', '0.5.0', versionsuffix)] -runtest = 'nosetests theano' +# The tests take very long to finish (they are installed too) +#runtest = 'nosetests theano' sanity_check_paths = { 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'math' -- GitLab From 599c684216887ad5d9a6f454bf3db375a527931a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 17:08:49 +0200 Subject: [PATCH 516/701] Fix remarks --- .../k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb | 2 +- .../p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb | 9 +++------ 2 files changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb index 76540365f0..418b1b87b0 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-1.0.8-intel-2016b-Python-3.5.2.eb @@ -22,7 +22,7 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb index 5e2dea3692..54aae7eafc 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb @@ -11,13 +11,10 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -pyver = '3.5.2' -pyshortver = '.'.join(pyver.split('.')[:2]) - -versionsuffix = '-Python-%s' % pyver +versionsuffix = '-Python-%(pyver)s' dependencies = [ - ('Python', pyver), + ('Python', '3.5.2'), ('libyaml', '0.1.6'), ] @@ -25,7 +22,7 @@ options = {'modulename': 'yaml'} sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/yaml' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'lib' -- GitLab From 9ab363ad6315fd6de5c35c5ff4d663fa56f482a2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 17:10:36 +0200 Subject: [PATCH 517/701] more remarks --- .../nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb index be6e199cd9..971304f89c 100644 --- a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-intel-2016b-Python-3.5.2.eb @@ -18,7 +18,7 @@ options = {'modulename': 'nose_parameterized'} sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/nose_parameterized-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'devel' -- GitLab From cf24b3d18693549f877296dda893df80bdfdf4b7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 20 Sep 2016 09:13:52 +0200 Subject: [PATCH 518/701] Fix remarks --- .../p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb index 54aae7eafc..266c49b425 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-3.5.2.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'PyYAML' version = '3.12' +versionsuffix = '-Python-%(pyver)s' homepage = "https://pypi.python.org/pypi/PyYAML/" description = """PyYAML is a YAML parser and emitter for the Python programming language.""" @@ -11,8 +12,6 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -versionsuffix = '-Python-%(pyver)s' - dependencies = [ ('Python', '3.5.2'), ('libyaml', '0.1.6'), -- GitLab From dccccacb41ba3de78ce1b7ea1e78f754b713441a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Sep 2016 10:36:36 +0200 Subject: [PATCH 519/701] add easyconfig ncview-2.1.7-intel-2016b.eb, add easyconfig UDUNITS-2.2.20-intel-2016b.eb --- .../n/ncview/ncview-2.1.7-intel-2016b.eb | 43 +++++++++++++++++++ .../u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb | 38 ++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb new file mode 100644 index 0000000000..09cf15c6d3 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.7' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(which $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.4.1'), + ('netCDF-Fortran', '4.4.4'), + ('UDUNITS', '2.2.20'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb new file mode 100644 index 0000000000..ae9bb8dae3 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.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, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# 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 = 'UDUNITS' +version = '2.2.20' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +dependencies = [('expat', '2.2.0')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' -- GitLab From ee90a03732e53231eebcb160b961e0b36e990706 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Sep 2016 11:18:05 +0200 Subject: [PATCH 520/701] disable testing in all ParaView 4.4.0 easyconfigs, don't hard specify optarch: True --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb | 2 +- .../easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb | 2 +- .../easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb | 2 +- easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb index 2130c99fd6..3f80a99e71 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb @@ -7,7 +7,7 @@ description = """HDF5 is a unique technology suite that makes possible the manag extremely large and complex data collections.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb index 358fff80d8..881a107e71 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-gimkl-2.11.5-mpi.eb @@ -41,7 +41,7 @@ configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBR configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb index c47c9437bd..5d0a411cd9 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b-mpi.eb @@ -41,7 +41,7 @@ configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBR configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb index bd0d7b5f22..ae3e6cddc3 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.4.0-intel-2015b.eb @@ -40,7 +40,7 @@ configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBR configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' configopts += '-DVTK_USE_SYSTEM_HDF5=ON ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.eb index 37afd28477..bf50049e0f 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2.11.5.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': 'gimkl', 'version': '2.11.5'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 9eb6a39aabc81168c93992762538c3b3e40769c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Sep 2016 14:55:41 +0200 Subject: [PATCH 521/701] add easyconfig tabix-0.2.6-intel-2016b.eb --- .../t/tabix/tabix-0.2.6-intel-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb new file mode 100644 index 0000000000..ef8197538d --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.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 +# Author: Jens Timmerman, Ghent University + +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': '2016b'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' -- GitLab From a3582c693dae1306caae0baa8e1eab43726b3a5d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Sep 2016 15:00:22 +0200 Subject: [PATCH 522/701] fix buildopts in tabix easyconfigs --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb | 4 ++-- 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 | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb index cb200231af..30c58df38b 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), @@ -29,4 +29,4 @@ sanity_check_paths = { 'dirs': [""], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' 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 4ab3c4b882..e138adfe4c 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 @@ -19,7 +19,7 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), 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 355e0eb0ad..af291cd25c 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 @@ -19,7 +19,7 @@ sources = [SOURCE_TAR_BZ2] dependencies = [('zlib', '1.2.8')] -buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' files_to_copy = [ (["tabix", "bgzip", "tabix.py"], "bin"), -- GitLab From a68f490cb9cd1d1ebcb4f2b489df724f9d76e3ac Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 20 Sep 2016 15:07:51 +0200 Subject: [PATCH 523/701] change according to intel2016b version --- .../Theano-0.8.2-foss-2016a-Python-2.7.11.eb | 21 +++++++++---------- .../Theano-0.8.2-foss-2016a-Python-3.5.1.eb | 21 +++++++++---------- 2 files changed, 20 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb index f9de6cacae..84985c3bcb 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-2.7.11.eb @@ -5,25 +5,24 @@ version = '0.8.2' versionsuffix = '-Python-%(pyver)s' 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': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [ - ('Python', '2.7.11'), - ('binutils', '2.25', '', ('GCCcore','4.9.3')), - ('Pygments', '2.1.3', versionsuffix), - ('Sphinx', '1.4.5', versionsuffix) -] +dependencies = [('Python', '2.7.11')] + +builddependencies = [('nose-parameterized', '0.5.0', versionsuffix)] + +# The tests take very long to finish (they are installed too) +#runtest = 'nosetests theano' sanity_check_paths = { - 'files': ['bin/theano-cache', - 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], - 'dirs': [] + 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'math' \ No newline at end of file diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb index 7049aceac7..07ee987f27 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb @@ -5,25 +5,24 @@ version = '0.8.2' versionsuffix = '-Python-%(pyver)s' 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': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [ - ('Python', '3.5.1'), - ('binutils', '2.25', '', ('GCCcore','4.9.3')), - ('Pygments', '2.1.3', versionsuffix), - ('Sphinx', '1.4.5', versionsuffix) -] +dependencies = [('Python', '3.5.2')] + +builddependencies = [('nose-parameterized', '0.5.0', versionsuffix)] + +# The tests take very long to finish (they are installed too) +#runtest = 'nosetests theano' sanity_check_paths = { - 'files': ['bin/theano-cache', - 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], - 'dirs': [] + 'files': ['bin/theano-cache', 'bin/theano-nose', 'bin/theano-test'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'math' \ No newline at end of file -- GitLab From 42ef02f4719e6a9fca27ed6b34a2b4c474cf1900 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 20 Sep 2016 15:09:47 +0200 Subject: [PATCH 524/701] nose-parameterized deps --- ...eterized-0.5.0-foss-2016a-Python-2.7.11.eb | 24 +++++++++++++++++++ ...meterized-0.5.0-foss-2016a-Python-3.5.2.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..ced9988f35 --- /dev/null +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'nose-parameterized' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'hmat://github.com/wolever/nose-parameterized' +description = """Parameterized testing with any Python test framework.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.11')] + +options = {'modulename': 'nose_parameterized'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.2.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.2.eb new file mode 100644 index 0000000000..881e0ecc4f --- /dev/null +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.2.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'nose-parameterized' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'hmat://github.com/wolever/nose-parameterized' +description = """Parameterized testing with any Python test framework.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +options = {'modulename': 'nose_parameterized'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' -- GitLab From 0325b915da57637954634533464684f4e7a06997 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 20 Sep 2016 15:55:14 +0200 Subject: [PATCH 525/701] change version of python for nose dep --- ...meterized-0.5.0-foss-2016a-Python-3.5.1.eb | 24 +++++++++++++++++++ .../Theano-0.8.2-foss-2016a-Python-3.5.1.eb | 4 ++-- 2 files changed, 26 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..6c5140ef8c --- /dev/null +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'nose-parameterized' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'hmat://github.com/wolever/nose-parameterized' +description = """Parameterized testing with any Python test framework.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.1')] + +options = {'modulename': 'nose_parameterized'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb index 07ee987f27..d7e9b83bcb 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.8.2-foss-2016a-Python-3.5.1.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('Python', '3.5.2')] +dependencies = [('Python', '3.5.1')] builddependencies = [('nose-parameterized', '0.5.0', versionsuffix)] @@ -25,4 +25,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' -- GitLab From 85ccbbcb40d38fdb5fd65217e9aeabca474e1070 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 20 Sep 2016 15:56:20 +0200 Subject: [PATCH 526/701] remove that version --- ...meterized-0.5.0-foss-2016a-Python-3.5.2.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.2.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.2.eb deleted file mode 100644 index 881e0ecc4f..0000000000 --- a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.5.0-foss-2016a-Python-3.5.2.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'nose-parameterized' -version = '0.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'hmat://github.com/wolever/nose-parameterized' -description = """Parameterized testing with any Python test framework.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [('Python', '3.5.2')] - -options = {'modulename': 'nose_parameterized'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' -- GitLab From 3bc8a3c863fa629105143af0d66926cf25cd708c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Sep 2016 18:50:13 +0200 Subject: [PATCH 527/701] also check 'lib' Tcl subdir for graphviz bindings --- .../easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb | 5 ++++- .../g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb index c85ed5ed21..4634a7fb1a 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb @@ -58,7 +58,10 @@ sanity_check_paths = { 'dirs': ['include', 'lib/graphviz'] } -sanity_check_commands = [("test ! -d $EBROOTTCL/lib64/*/graphviz", '')] +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), +] modextrapaths = { 'PYTHONPATH': 'lib/graphviz/python', diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index 88594633da..c9fd0d8f27 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -60,7 +60,10 @@ sanity_check_paths = { 'dirs': ['include', 'lib/graphviz'] } -sanity_check_commands = [("test ! -d $EBROOTTCL/lib64/*/graphviz", '')] +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), +] modextrapaths = { 'PYTHONPATH': 'lib/graphviz/python', -- GitLab From 74ca35651427b0688819ca02ae0e1605a56d4e99 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Sep 2016 20:12:08 +0200 Subject: [PATCH 528/701] {lang,lib}[GCC/4.8.4] Python 2.7.9 (bare) + libxml2 2.9.2 --- .../b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb | 15 ++++++++ .../libreadline/libreadline-6.3-GCC-4.8.4.eb | 31 +++++++++++++++ .../l/libxml2/libxml2-2.9.2-GCC-4.8.4.eb | 20 ++++++++++ .../p/Python/Python-2.7.9-GCC-4.8.4-bare.eb | 31 +++++++++++++++ .../s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb | 38 +++++++++++++++++++ .../easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.8.4.eb | 25 ++++++++++++ .../t/Tk/Tk-8.6.3-GCC-4.8.4-no-X11.eb | 26 +++++++++++++ .../z/zlib/zlib-1.2.8-GCC-4.8.4.eb | 21 ++++++++++ 8 files changed, 207 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.8.4-no-X11.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb new file mode 100644 index 0000000000..0a99a45a08 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.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': 'GCC', 'version': '4.8.4'} +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-GCC-4.8.4.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb new file mode 100644 index 0000000000..50303a9e80 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb @@ -0,0 +1,31 @@ +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': 'GCC', 'version': '4.8.4'} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '5.9')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +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/libxml2/libxml2-2.9.2-GCC-4.8.4.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.4.eb new file mode 100644 index 0000000000..25e24ba97f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.4.eb @@ -0,0 +1,20 @@ +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': '4.8.4'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb new file mode 100644 index 0000000000..c83dff187b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-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': 'GCC', 'version': '4.8.4'} +toolchainopts = {'pic': 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'), + ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack + #('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')] + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb new file mode 100644 index 0000000000..27cd84d7ec --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.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': 'GCC', 'version': '4.8.4'} + +# 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-GCC-4.8.4.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.8.4.eb new file mode 100644 index 0000000000..d3061eabd1 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.8.4.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': 'GCC', 'version': '4.8.4'} + +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-8.6.3-GCC-4.8.4-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.8.4-no-X11.eb new file mode 100644 index 0000000000..e49d801973 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.8.4-no-X11.eb @@ -0,0 +1,26 @@ +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': 'GCC', 'version': '4.8.4'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +# To be clear: this will still require X11 to be present (see issue #2261) +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb new file mode 100644 index 0000000000..020b89196b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.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': '4.8.4'} + +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 3288fa46ea6c37f2c2458bbb495f10fd8943c91e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Sep 2016 20:42:34 +0200 Subject: [PATCH 529/701] consistently enable -fPIC for libreadline and zlib --- easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb | 1 + easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb | 1 + easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb | 1 + easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb | 1 + easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb | 1 + easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb | 1 + 6 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb index 55d005e4b8..3d2321bd06 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.2.eb @@ -10,6 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb index 50303a9e80..25cb143653 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.8.4.eb @@ -10,6 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'GCC', 'version': '4.8.4'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb index 53eeab2af9..36625b1717 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb @@ -10,6 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb index 1c29958289..1192872c10 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb @@ -9,6 +9,7 @@ not covered by any patents -- lossless data-compression library for use on virtu computer hardware and operating system.""" toolchain = {'name': 'GCC', 'version': '4.7.3'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb index 020b89196b..d7207b104a 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.4.eb @@ -9,6 +9,7 @@ not covered by any patents -- lossless data-compression library for use on virtu computer hardware and operating system.""" toolchain = {'name': 'GCC', 'version': '4.8.4'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb index 82a1155e2e..ec9d1a0bdf 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb @@ -9,6 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -- GitLab From 16dca9802d16e3791e3dd312b183afbc17d57ce8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 20 Sep 2016 23:56:42 +0100 Subject: [PATCH 530/701] add easyconfig libibmad-1.3.12-GCC-4.9.3-2.25.eb, add easyconfig libibumad-1.3.10.2-GCC-4.9.3-2.25.eb --- .../libibmad-1.3.12-GCC-4.9.3-2.25.eb | 24 +++++++++++++++++++ .../libibumad-1.3.10.2-GCC-4.9.3-2.25.eb | 19 +++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/l/libibmad/libibmad-1.3.12-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libibumad/libibumad-1.3.10.2-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/l/libibmad/libibmad-1.3.12-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libibmad/libibmad-1.3.12-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..d619aa0f82 --- /dev/null +++ b/easybuild/easyconfigs/l/libibmad/libibmad-1.3.12-GCC-4.9.3-2.25.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libibmad' +version = '1.3.12' + +homepage = 'http://www.openfabrics.org' +description = """libibmad is a convenience library to encode, decode, and dump IB MAD packets. It + is implemented on top of and in conjunction with libibumad (the umad kernel + interface library.)""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.openfabrics.org/downloads/management/'] + +dependencies = [('libibumad', '1.3.10.2')] + +sanity_check_paths = { + 'files': ['include/infiniband/mad.h', 'include/infiniband/mad_osd.h', + 'lib/libibmad.a', 'lib/libibmad.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libibumad/libibumad-1.3.10.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libibumad/libibumad-1.3.10.2-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..c2063cef0d --- /dev/null +++ b/easybuild/easyconfigs/l/libibumad/libibumad-1.3.10.2-GCC-4.9.3-2.25.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libibumad' +version = '1.3.10.2' + +homepage = 'http://www.openfabrics.org' +description = """libibumad is the umad kernel interface library.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.openfabrics.org/downloads/management/'] + +sanity_check_paths = { + 'files': ['include/infiniband/umad.h', 'lib/libibumad.a', 'lib/libibumad.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'system' -- GitLab From e66be064481fe46e047d50e20e275ec9412d3b98 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 21 Sep 2016 12:04:20 +0800 Subject: [PATCH 531/701] comment out patch files --- .../v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 92a0ece294..4b2a8bbb84 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -14,12 +14,12 @@ toolchainopts = {'usempi': True} # Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code sources = [SOURCELOWER_TAR_GZ] -# patches from http://cms.mpi.univie.ac.at/wiki/index.php/Installing_VASP -patches = [ - 'vasp.5.4.1.08072015.patch', - 'vasp.5.4.1.27082015.patch', - 'vasp.5.4.1.06112015.patch', -] +# uncommment after downloading patches from http://cms.mpi.univie.ac.at/wiki/index.php/Installing_VASP +#patches = [ +# 'vasp.5.4.1.08072015.patch', +# 'vasp.5.4.1.27082015.patch', +# 'vasp.5.4.1.06112015.patch', +#] checksums = [ '57c2b07d0f70987000033984e913f1a6', # vasp.5.4.1.tar.gz -- GitLab From c156c0bb0a07c39bf429ef70ed321de048e79a08 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 21 Sep 2016 12:45:42 +0200 Subject: [PATCH 532/701] Qhull 2015.2 compiled using the foss 2016a toolchain. --- .../q/Qhull/Qhull-2015.2-foss-2016a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb new file mode 100644 index 0000000000..c145ad7bf0 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2015.2' + +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': 'foss', 'version': '2016a'} + +# Recently changed the Unix version numbering see http://www.qhull.org/src/Changes.txt +# and https://github.com/Homebrew/homebrew-science/issues/3353 +sources = ['%(namelower)s-%(version_major)s-src-7.%(version_minor)s.0.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = [ + 'Qhull_pkgconfig.patch', +] + +builddependencies = [('CMake', '3.4.3')] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.%s' % SHLIB_EXT, 'lib/pkgconfig/qhull.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' -- GitLab From ad9d3836a8aa906c7e2e7273a0af0ca7db9841b0 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 21 Sep 2016 12:47:57 +0200 Subject: [PATCH 533/701] networkx 1.11 compiled using the foss 2016a toolchain. --- .../networkx-1.11-foss-2016a-Python-2.7.11.eb | 25 +++++++++++++++++++ .../networkx-1.11-foss-2016a-Python-3.5.1.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..8dde76eb25 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.11' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..488dd6f650 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.11' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'tools' -- GitLab From c91a49102e2aafe0378d70744728e5a6cf39c614 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 21 Sep 2016 13:43:53 +0200 Subject: [PATCH 534/701] Easyconfig for angsd 0.910 using the foss 2016a toolchain. --- .../a/angsd/angsd-0.910-foss-2016a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb b/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb new file mode 100644 index 0000000000..c9d9db6e85 --- /dev/null +++ b/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'angsd' +version = '0.910' + +homepage = 'http://www.popgen.dk/angsd' +description = """Program for analysing NGS data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/ANGSD/angsd/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('HTSlib', '1.3.1')] + +files_to_copy = [ + (['angsd'], 'bin'), + 'doc', +] + +sanity_check_paths = { + 'files': ['bin/angsd'], + 'dirs': ['doc'], +} + +moduleclass = 'bio' -- GitLab From 756020ca9264280c31b2c1eb229cd1fe9c531a99 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Sep 2016 17:02:34 +0200 Subject: [PATCH 535/701] Add missing dependency on XZ to libxml2. The original problem is that when building libxml2 on a system with liblzma installed by the distro, it picks up dependencies on lzma routines. Some of the versions of Gromacs are linking against libxml2 statically, causing link errors agains lzma. And any other software that does static linking against libxml2 will have the same problem. There is a cyclic dependency between XZ, libxml2, and gettext. Fix this by adding a dummy toolchain build of gettext without any dependencies on anything. XZ for the updated toolchains are then built with the dummy-toolchain gettext as a build dependency. And then normal toolchain builds of libxml2 (now with XZ dependency) and gettext can be built against that XZ. This was originally discussed in issue #3408. --- .../easyconfigs/g/gettext/gettext-0.19.8.eb | 23 +++++++++++++++ .../l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb | 5 +++- .../l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb | 1 + .../l/libxml2/libxml2-2.9.4-foss-2016.04.eb | 5 +++- .../l/libxml2/libxml2-2.9.4-foss-2016b.eb | 5 +++- ...libxml2-2.9.4-intel-2016b-Python-2.7.12.eb | 1 + .../l/libxml2/libxml2-2.9.4-intel-2016b.eb | 5 +++- .../x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb | 27 ++++++++++++++++++ .../x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb | 28 +++++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb | 5 +--- .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb | 5 +--- .../easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb | 5 +--- 12 files changed, 99 insertions(+), 16 deletions(-) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb new file mode 100644 index 0000000000..ac95067f78 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8' + +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""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb index 6000926382..798eea2998 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb @@ -14,6 +14,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb index 6e41adde06..4873fafcda 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb @@ -21,6 +21,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.8'), + ('XZ', '5.2.2'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb index 645a9c0d23..9268fd68be 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016.04.eb @@ -15,6 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb index 09ede640fb..abee889e32 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.eb @@ -15,6 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb index d2e63d779b..5f9093db10 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b-Python-2.7.12.eb @@ -17,6 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('zlib', '1.2.8'), + ('XZ', '5.2.2'), ('Python', '2.7.12'), ] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb index b41d38c545..ab1c0ecd3e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.eb @@ -15,6 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..9d2ac5e32d --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', '0.19.8', '', True), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb new file mode 100644 index 0000000000..cafe4d07ac --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', '0.19.8', '', True), + ('binutils', '2.25'), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb index 0faab98c7c..6d7bd28197 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.8'), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb index cd78959323..8bddb8fe4a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.8'), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb index f05bff12d4..7d1af0e121 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.8'), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs -- GitLab From d2ba6ece582383f7208a52d0c236cd3a11d82645 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 21 Sep 2016 15:27:02 +0200 Subject: [PATCH 536/701] GDAL 2.1.1 for foss-2016a --- .../g/GDAL/GDAL-2.1.1-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000..0ec6ce953a --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.1' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.4.0'), + ('expat', '2.1.1'), + ('libxml2', '2.9.3'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' -- GitLab From 6ca22778637c7a562dbd95c245f223819bb82984 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 21 Sep 2016 15:35:12 +0200 Subject: [PATCH 537/701] Add XZ dependency to libxml2-2.9.4-foss-2016a too. Add required dummy toolchain versions of gettext-0.19.6 and .7 --- .../easyconfigs/g/gettext/gettext-0.19.6.eb | 23 +++++++++++++++++++ .../easyconfigs/g/gettext/gettext-0.19.7.eb | 23 +++++++++++++++++++ .../l/libxml2/libxml2-2.9.4-foss-2016a.eb | 5 +++- .../XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb | 9 +++----- .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 5 +--- 5 files changed, 54 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb new file mode 100644 index 0000000000..fd9544cda7 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.6' + +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""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb new file mode 100644 index 0000000000..cfca8144b6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.7' + +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""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb index e6cae21695..7b6aba23a4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb @@ -15,6 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb index 17cd0492c0..b4a5a18d70 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb @@ -11,15 +11,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -builddependencies = [ - ('Autotools', '20150215'), -] - gettext_ver = '0.19.7' versionsuffix = '-gettext-%s' % gettext_ver -dependencies = [ - ('gettext', gettext_ver), +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', gettext_ver, '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb index 2a89ca6af6..9cb0eb5b87 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.6'), + ('gettext', '0.19.6', '', True), ] # may become useful in non-x86 archs -- GitLab From f34f4a8f88c36b97773579adbe971236c6631349 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 21 Sep 2016 15:41:43 +0200 Subject: [PATCH 538/701] Fix typo in "Add XZ dependency to libxml2-2.9.4-foss-2016a too." --- easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb index 7b6aba23a4..59cbe77a84 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.eb @@ -18,6 +18,6 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('zlib', '1.2.8'), ('XZ', '5.2.2'), -} +] moduleclass = 'lib' -- GitLab From d46a3bfa4f15d2dfd086309c42b658e71ad3a143 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 21 Sep 2016 15:59:16 +0200 Subject: [PATCH 539/701] Update remaining XZ-5.2.2- files to have a build dependency on a dummy-toolchain gettext instead of a run time dependency on a toolchain gettext. --- .../easyconfigs/g/gettext/gettext-0.18.2.eb | 23 +++++++++++++++++++ .../easyconfigs/g/gettext/gettext-0.19.4.eb | 23 +++++++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb | 5 +--- .../easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb | 5 +--- .../easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb | 5 +--- .../XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb | 9 +++----- .../easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 5 +--- 7 files changed, 53 insertions(+), 22 deletions(-) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb new file mode 100644 index 0000000000..ca42caa817 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.18.2' + +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""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb new file mode 100644 index 0000000000..23ce1e2b27 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb @@ -0,0 +1,23 @@ +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""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb index 049e77b657..0245b4d813 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.4'), + ('gettext', '0.19.4', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb index f9a06be732..c463ba319e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215', '', ('GCC', '4.7.2')), -] - -dependencies = [ - ('gettext', '0.18.2'), + ('gettext', '0.18.2', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb index 96fe0ea8c8..3e8e48f760 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.18.2'), + ('gettext', '0.18.2', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb index 7953b85916..b10cbfb5b1 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb @@ -11,15 +11,12 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -builddependencies = [ - ('Autotools', '20150215'), -] - gettext_ver = '0.19.7' versionsuffix = '-gettext-%s' % gettext_ver -dependencies = [ - ('gettext', gettext_ver), +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', gettext_ver, '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index b717af018a..e582d9cc6b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -13,10 +13,7 @@ source_urls = ['http://tukaani.org/xz/'] builddependencies = [ ('Autotools', '20150215'), -] - -dependencies = [ - ('gettext', '0.19.6'), + ('gettext', '0.19.6', '', True), ] # may become useful in non-x86 archs -- GitLab From e1de06402c85222d4bd26ae19ef6e4094df12679 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 21 Sep 2016 16:16:41 +0200 Subject: [PATCH 540/701] QCA-2.1.0 foss 2016a --- .../easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb new file mode 100644 index 0000000000..6422b82abe --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.0-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' +name = 'QCA' +version = '2.1.0' + +homepage = 'http://delta.affinix.com/qca/' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://delta.affinix.com/download/qca/2.0/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +configopts = "-DQT4_BUILD=true" + +builddependencies = [ + ('CMake', '3.5.2') +] + +dependencies = [ + ('Qt', '4.8.7') +] + +moduleclass = 'devel' -- GitLab From 654c378df4f96e59f3eefcea4ba61b550089f79b Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 21 Sep 2016 16:32:47 +0200 Subject: [PATCH 541/701] missing sip --- .../PyQt-4.11.4-foss-2016a-Python-2.7.11.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..4f44ed007d --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,41 @@ +# 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': '2016a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.11' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.7'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +moduleclass = 'vis' -- GitLab From 8284ce4db99bd7304efc1cc3f752760593c358c6 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 21 Sep 2016 16:34:28 +0200 Subject: [PATCH 542/701] SIP 4.18 foss 2016a$ --- .../SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..0ac8c1861d --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +# 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 = '4.18' +versionsuffix = '-Python-%(pyver)s' + +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': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.11')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 1a3e2c84910a6df7f4524aaed7a43a774919c070 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 21 Sep 2016 17:05:06 +0200 Subject: [PATCH 543/701] cleanup --- .../PyQt-4.11.4-foss-2016a-Python-2.7.11.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2016a-Python-2.7.11.eb deleted file mode 100644 index 4f44ed007d..0000000000 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,41 +0,0 @@ -# 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': '2016a'} - -sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] -source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] - -python = 'Python' -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-%s-%s' % (python, pyver) - -dependencies = [ - (python, pyver), - ('SIP', '4.16.8', versionsuffix), - ('Qt', '4.8.7'), -] - -configopts = "configure-ng.py --confirm-license" -configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver -configopts += " --no-sip-files" - -options = {'modulename': '%(name)s%(version_major)s'} - -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], -} - -moduleclass = 'vis' -- GitLab From c849c699384d548feb18b72ab5b4f1c637bcf313 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 21 Sep 2016 17:47:56 +0200 Subject: [PATCH 544/701] Fix bad config option for dummy-toolchain gettext. Use the correct configure option to use the internal libxml. And keep the dependencies as close to the normal tool-chain versions as possible. --- easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb | 4 +++- easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb | 4 +++- 5 files changed, 9 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb index ca42caa817..68b4d25ce9 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb @@ -18,6 +18,6 @@ toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb index 23ce1e2b27..ed81b95755 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb @@ -18,6 +18,6 @@ toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb index fd9544cda7..ce355420b2 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb @@ -18,6 +18,6 @@ toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb index cfca8144b6..578b07b38d 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' +dependencies = [('ncurses', '6.0')] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb index ac95067f78..45caa1fde8 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = '--without-emacs --without-libxml2-prefix --without-libncurses-prefix --without-xz --without-bzip2' +dependencies = [('ncurses', '6.0')] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' moduleclass = 'vis' -- GitLab From 8fe44ea98e79db6759715c96ad327c8caf32e77e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 22 Sep 2016 15:58:42 +0800 Subject: [PATCH 545/701] change filename and checksum --- .../easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb index 4b2a8bbb84..5cd635730b 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'usempi': True} # Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code -sources = [SOURCELOWER_TAR_GZ] +sources = ['vasp.5.4.1.24Jun15.tar.gz'] # uncommment after downloading patches from http://cms.mpi.univie.ac.at/wiki/index.php/Installing_VASP #patches = [ @@ -22,7 +22,7 @@ sources = [SOURCELOWER_TAR_GZ] #] checksums = [ - '57c2b07d0f70987000033984e913f1a6', # vasp.5.4.1.tar.gz + '9a56174e272ac0c07645c42932848788', # vasp.5.4.1.24Jun15.tar.gz 'ee242452bba6bb37459745f4617649d7', # vasp.5.4.1.08072015.patch 'b137eb13804a60df382e77495dc738f9', # vasp.5.4.1.27082015.patch 'd64b8f0ae861db7a76e6e9c9ffa188a1', # vasp.5.4.1.06112015.patch -- GitLab From 8d5077afbc9d0e82b7ed0db6ad43ee3ddf4d8817 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Sep 2016 15:12:40 +0200 Subject: [PATCH 546/701] Revert "Removing LeadIT from this PR" This reverts commit d470e60f9ba9c5218e13f190a98f7b5bd137bc5a. --- .../easyconfigs/l/LeadIT/LeadIT-2.1.9.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb diff --git a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb new file mode 100644 index 0000000000..128c5bbc07 --- /dev/null +++ b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'LeadIT' +version = '2.1.9' + +homepage = 'http://www.biosolveit.de/LeadIT/index.html' +description = """Visually Informed LeadOpt""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +#You need to get the software manually from http://www.biosolveit.de/LeadIT/index.html +sources = ['leadit-%(version)s-Linux-x64.tar.gz'] + +checksums = ['363fa557861c4d109fd595ab895df3fd'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["leadit", "flexv", "hydescorer"], + 'dirs': ["example", "doc"] +} + +moduleclass = 'chem' -- GitLab From 256b80ea87b763a1d2fe7b7aa29a32de43b75e5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Sep 2016 15:27:36 +0200 Subject: [PATCH 547/701] bump version to 2.9.0 & update release notes --- RELEASE_NOTES | 56 +++++++++++++++++++++++++++++++++++++++++++++++++-- setup.py | 2 +- 2 files changed, 55 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 8501454d37..c74d917ce1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,60 @@ 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 6,548 easyconfig files, for 998 different software packages, -37 different (compiler) toolchains, 12 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 7,060 easyconfig files, for 1,085 different software packages, +37 different (compiler) toolchains, 13 software bundles and 1 meta-package. + +v2.9.0 (September 23rd 2016) +---------------------------- + +feature release +- added example easyconfig files for 88 new software packages: + ADMIXTURE (#3359), angsd (#3593), ASHS (#3429), AutoDock (#3465), AutoGrid (#3466), BayeScan (#2748, #3356), + BayPass (#3451), Bazel (#3379), Blender (#3553, #3558), bwakit (#3567), BXH_XCEDE_TOOLS (#3410), CastXML (#3403), + CHASE (#3304), configparser (#3368, #3424), configurable-http-proxy (#3380), cppcheck (#3508), CRPropa (#779), + DicomBrowser (#3432), DMTCP (#3422), entrypoints (#3368, #3424), f90cache (#3570), fastPHASE (#3343), + fastQValidator (#3192), FFindex (#1135), FragGeneScan (#1198), gdc-client (#3399), gflags (#3417), glog (#3417), + GRIT (#3561), H5hut (#3431), HAPGEN2 (#3344), HEALPix (#779), IMOD (#1187, #3347), IronPython (#607), + jhbuild (#3476), jupyterhub (#3380), Keras (#3581), khmer (#1158), LeadIT (#3345, #3599), LevelDB (#3417), + libbitmask (#3481), libcpuset (#3481), LMDB (#3417), log4cplus (#1136), MACH (#3346), Mako (#3460), Maq (#3428), + MetaGeneAnnotator (#3307), Metal (#3324), Mono (#607), MyMediaLite (#607), nco (#2575), nose-parameterized (#3579), + OpenEXR (#3553), OpenImageIO (#3553), path.py (#3368, #3424), PCRE2 (#3325), pftoolsV3 (#3317), PHASE (#3385), + PLAST (#3288), PLINKSEQ (#3402), POV-Ray (#3551), ProbABEL (#3108), prompt-toolkit (#3368, #3424), + protobuf-python (#3563), PSORTb (#3317), py (#3403, #3482), pygccxml (#3403, #3482), pyGIMLi (#3403, #3482), + pyplusplus (#3403, #3482), PyQt5 (#3533), Pyro4 (#3527), pytest (#3403, #3482), QCA (#3595), RDMC (#1137), + S.A.G.E. (#3427), SDL2 (#3551), SHORE (#3531), SimVascular (#3555), SortMeRNA (#3326), SUMACLUST (#3316), + SUMATRA (#3316), Text-CSV (#3323), Triangle (#3403), VEGAS (#3457), VirSorter (#3307), wcwidth (#3368, #3424), + X11 (#3340) +- added new easyconfigs for existing toolchains: + - CrayGNU + CrayIntel 2016.06 (#3377) + - foss 2016.07 (#3517) + 2016.09 (#3523), + - iomkl 2016.07 (#3458) + - pomkl 2016.09 (#3516) +- added additional easyconfigs for various supported software packages, including: + FFTW 3.3.5, GCC 4.9.4 + 6.2.0, GROMACS 5.1.4, IPython 5.1.0, LLVM 3.9.0, Mesa 12.0.1, OpenCV 3.1.0, OpenFOAM 4.0, + OpenMPI 2.0.1, ParaView 5.1.2, PGI 16.7, QuantumESPRESSO 5.4.0, Qt5 5.7.0, R-bundle-Bioconductor 3.3, VTK 7.0.0, + Yade 2016.06a +- various enhancements, including: + - adjust PSI4 easyconfigs for updated easyblock (#3312) + - clean up libxml2 easyconfigs according to updated libxml2 easyblock (#3479, #3509) + - significantly speed up verifying of dumped easyconfig by resorting to 'shallow' parsing (#3520) + - include sanity checks for all MATIO config files (#3528) + - remove --with-tcl-config/--with-tk-config from R easyconfig, already done in R easyblock (#3580) +- various bug fixes, including: + - disable testing in all ParaView 4.4.0 easyconfigs, required download is too much of a PITA (#3178) + - add SQLite as dep to GDAL 2.1.0 easyconfigs (#3342) + - add zlib/SQLite/LibTIFF as dep to R 3.3.1 easyconfigs (#3342) + - add bzip2 as a dependency of freetype (#3464) + - specify correct MPI target in FDS easyconfigs (#3488) + - add tcsh as OS dep in NAMD easyconfigs (#3491) + - statically link ncurses/libreadline in Lua easyconfig with 'dummy' toolchain (#3545) + - add M4 as dep for flex 2.6.x (#3542, #3550) + - add bzip2 and libxcb dependencies to FFmpeg 3.x easyconfigs (#3548) + - make sure & check that Graphviz does not install Tcl bindings in Tcl install prefix (#3556) + - add missing patches for extensions in Python 3.x easyconfigs (#3557) + - add missing XZ dependency to libxml2 2.9.4 easyconfigs, change gettext dep of XZ to build-only dep (#3568) + - enable running of tests for HPCG (#3578) + - fix buildopts in tabix easyconfigs (#3584) v2.8.2 (July 13th 2016) diff --git a/setup.py b/setup.py index c52c2d0550..4a7ed9800b 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.9.0.dev0' +VERSION = '2.9.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 5967479a1f949dad7bb3a8fa65f26450053a6232 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 23 Sep 2016 14:41:29 +0200 Subject: [PATCH 548/701] Add FLUENT/17.1 --- easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb new file mode 100644 index 0000000000..c1ec088d35 --- /dev/null +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb @@ -0,0 +1,14 @@ +name = 'FLUENT' +version = '17.1' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' +description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed +to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from +air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, +from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['FLUIDS_171_LINX64.tar'] + +moduleclass = 'cae' -- GitLab From 58c0ed35527df8e39beffad7a46bb5413c0e6d04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2016 15:23:48 +0200 Subject: [PATCH 549/701] bump version to 3.0.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 4a7ed9800b..f4cbb44d3b 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '2.9.0' +VERSION = '3.0.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 01f7d3772abfa79c936597642dabec3063d3b620 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2016 15:31:22 +0200 Subject: [PATCH 550/701] add easyconfig EasyBuild-2.9.0.eb --- .../e/EasyBuild/EasyBuild-2.9.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb new file mode 100644 index 0000000000..09a04b73a8 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.9.0' + +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 = [ + # vsc-install + 'https://pypi.python.org/packages/0e/83/4ed8215c5b27ba4ee4a6da3d43ce9579b67c5fe7a91f33f48991f878db13/', + # vsc-base + 'https://pypi.python.org/packages/2b/fd/e16d723389f692b107b5e4e6243379d2b056e79a7ea3b5e4fdc2753d9541/', + # easybuild-framework + 'https://pypi.python.org/packages/e9/c7/da05d522cfc8b932956e77bdbf5270a91443df1f91bc2004a08776bd55da/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/0f/c4/65f98c2dc041e8201a51d2be61ec407e421f02e4f43775c7cb85ed4b8bcd/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/0a/5e/a0faffd999833c9f745b0f5592a8bce51556a4604d90daeda024244fa6fe/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.15.tar.gz', + 'vsc-base-2.5.4.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 4658d115ab82af90d7a48ba18ad0c3a0129e4623 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 24 Sep 2016 10:14:10 +0200 Subject: [PATCH 551/701] fix source URL in GCCcore 6.2.0 easyconfig --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 011920e0f4..3e675b3b89 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.4' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gcc/gcc-%(versions)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 -- GitLab From c18e1d1cc278d55205d819a0627623cab2bd9923 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 24 Sep 2016 10:17:02 +0200 Subject: [PATCH 552/701] fix typo --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 3e675b3b89..a375f0e539 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.4' source_urls = [ - 'http://ftpmirror.gnu.org/gcc/gcc-%(versions)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gcc/gcc-%(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 -- GitLab From 0e9b1e6adb1076a1d716ba11ab47b31e2b8071bf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 26 Sep 2016 12:16:07 +0200 Subject: [PATCH 553/701] add easyconfig Reads2snp-2.0.eb --- .../easyconfigs/r/Reads2snp/Reads2snp-2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb diff --git a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb new file mode 100644 index 0000000000..102136d546 --- /dev/null +++ b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'Reads2snp' +version = '2.0' + +homepage = 'http://kimura.univ-montp2.fr/PopPhyl/index.php?section=tools' +description = """reads2snp is a SNP and genotype caller: it predicts the genotype of distinct individuals + at distinct positions of a set of sequences based on read mapping / read counts. Its typical input is a bam file. + Its typical output is a vcf file. It is written in C++, based on the bio++ libraries, multi-threaded with openMP, + available under Linux and MacOS""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://kimura.univ-montp2.fr/PopPhyl/resources/tools/'] +sources = ['%(namelower)s_%(version)s.zip'] + +sanity_check_paths = { + 'files': ['reads2snp_2.0.64.bin'], + 'dirs': [], +} + +modextrapaths = { + 'PATH': "", # add the installation dir to PATH +} + +# disable exec permission for the provided 32 bits binary +postinstallcmds = ['chmod -x %(installdir)s/reads2snp_%(version)s.32.bin'] + +moduleclass = 'bio' -- GitLab From 6485f820e171394672f38700b71482876265612e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 26 Sep 2016 12:21:10 +0200 Subject: [PATCH 554/701] Add SWIG/3.0.8 for Python/2.7.12 --- .../SWIG-3.0.8-intel-2016b-Python-2.7.12.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..00ac605f8c --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.8' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' -- GitLab From aa6655d9d4b24b3ff9c5b5fab2be7d61557c106a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 26 Sep 2016 12:21:26 +0200 Subject: [PATCH 555/701] Added PLplot/5.11.1 for intel/2016b --- ...intel-2016b-Java-1.7.0_80-Python-2.7.12.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb new file mode 100644 index 0000000000..837821c853 --- /dev/null +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'PLplot' +version = '5.11.1' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'http://plplot.sourceforge.net' +description = """PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols + and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.6.1'), + ('SWIG', '3.0.8', '-Python-%(pyver)s'), + ('libtool', '2.4.6'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Java', '1.7.0_80', '', True), + ('Python', '2.7.12'), + ('Perl', '5.24.0'), + ('cairo', '1.14.6'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('X11', '20160819'), + ('Pango', '1.40.3'), + ('pixman', '0.34.0'), + ('Tcl', '8.6.5'), + ('Tk', '8.6.5'), +] + +separate_build_dir = True + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libplplot.so', 'lib/pkgconfig/plplot-f95.pc'], + 'dirs': ['bin', 'include/plplot', 'lib/fortran/modules/plplot', 'lib/pkgconfig', 'share/man/man1'], +} + +moduleclass = 'vis' -- GitLab From 6037845e53673227ec71cfe5946df32d21a6381e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 26 Sep 2016 12:31:28 +0200 Subject: [PATCH 556/701] Resolve conflict --- .../PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb | 2 +- .../easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb index 837821c853..e8ab2cacc4 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.6.1'), - ('SWIG', '3.0.8', '-Python-%(pyver)s'), + ('SWIG', '3.0.10', '-Python-%(pyver)s'), ('libtool', '2.4.6'), ] diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb index fed2dcb3c3..383771a5de 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.12'), - ('PCRE', '8.38'), + ('PCRE', '8.39'), ] moduleclass = 'devel' -- GitLab From c1b54df0f8632d0ac9aba60a1d93949ca2df0b36 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 26 Sep 2016 13:11:51 +0200 Subject: [PATCH 557/701] scikit-image built with the foss-2016a toolchain, including the Pillow dependency. --- .../Pillow-3.2.0-foss-2016a-Python-2.7.11.eb | 27 +++++++++++++++ ...t-image-0.12.3-foss-2016a-Python-2.7.11.eb | 33 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..b7a1d9ade1 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.2.0' +versionsuffix = '-Python-%(pyver)s' + +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': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('libjpeg-turbo', '1.4.2','-NASM-2.12.01'), + ('libpng', '1.6.21'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', '2.6.3'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..fd95fa30d2 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'scikit-image' +version = '0.12.3' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('Qhull', '2015.2'), + ('matplotlib', '1.5.1', versionsuffix), + ('networkx', '1.11', versionsuffix), + ('Pillow', '3.2.0', versionsuffix), +] + +options = {'modulename': 'skimage'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' -- GitLab From 235c7ccbdd3e196b02d56bb6907afd0c8e4ad4e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Sep 2016 13:28:47 +0200 Subject: [PATCH 558/701] correct STAMP dependency in i-cisTarget, must be 1.3 --- ...rget-20160602-intel-2016a-Python-2.7.11.eb | 2 +- .../s/STAMP/STAMP-1.2-intel-2016a.eb | 4 +-- .../s/STAMP/STAMP-1.3-intel-2016a.eb | 27 +++++++++++++++++++ 3 files changed, 30 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb diff --git a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb index 5d57424030..efeb188af2 100644 --- a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -41,7 +41,7 @@ dependencies = [ ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3'), ('MySQL-python', '1.2.5', versionsuffix + '-MariaDB-10.1.14'), ('ImageMagick', '6.9.4-8'), - ('STAMP', '1.2'), + ('STAMP', '1.3'), ('Cluster-Buster', '20160106'), ('Kent_tools', '20130806', '-linux.x86_64', True), ] diff --git a/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb index 117f2476d8..1794e98775 100644 --- a/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb @@ -3,12 +3,12 @@ easyblock = 'CmdCp' name = 'STAMP' version = '1.2' -homepage = 'ihttp://www.benoslab.pitt.edu/stamp/ - https://github.com/aertslab/stamp' +homepage = 'http://www.benoslab.pitt.edu/stamp/' description = """STAMP is a tool for characterizing similarities between transcription factor binding motifs""" toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https://github.com/aertslab/stamp/archive/'] +source_urls = ['https://github.com/seqcode/stamp/archive/'] sources = ['v%(version)s.tar.gz'] dependencies = [('GSL', '2.1')] diff --git a/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb new file mode 100644 index 0000000000..8ab4c4024a --- /dev/null +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'CmdCp' + +name = 'STAMP' +version = '1.3' + +homepage = 'http://www.benoslab.pitt.edu/stamp/' +description = """STAMP is a tool for characterizing similarities between transcription factor binding motifs""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/seqcode/stamp/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GSL', '2.1')] + +start_dir = 'src' + +cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp -lm -lgsl -lgslcblas")] + +files_to_copy = [(['stamp'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stamp'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c662a3cd5dfe3f361202eb565427bec82d28c70c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Sep 2016 13:50:32 +0200 Subject: [PATCH 559/701] add easyconfig HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb --- ...HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..12d319ea7b --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'HTSeq' +version = '0.6.1p1' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': '%(name)s'} + +sanity_check_paths = { + 'files': ['bin/htseq-count', 'bin/htseq-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From 23364fcb3c8d51afe66caf5f1ce2876e53070f47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Sep 2016 14:03:10 +0200 Subject: [PATCH 560/701] also include $LDFLAGS in compiler command for STAMP --- easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb index 1794e98775..f3009cafcc 100644 --- a/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb @@ -15,7 +15,7 @@ dependencies = [('GSL', '2.1')] start_dir = 'src' -cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp -lm -lgsl -lgslcblas")] +cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp $LDFLAGS -lm -lgsl -lgslcblas")] files_to_copy = [(['stamp'], 'bin')] diff --git a/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb index 8ab4c4024a..57a2608b75 100644 --- a/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb @@ -15,7 +15,7 @@ dependencies = [('GSL', '2.1')] start_dir = 'src' -cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp -lm -lgsl -lgslcblas")] +cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp $LDFLAGS -lm -lgsl -lgslcblas")] files_to_copy = [(['stamp'], 'bin')] -- GitLab From adb7061ed2148cff1a0e66134b20e320da2d6dc5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Sep 2016 16:30:10 +0200 Subject: [PATCH 561/701] add STAMP 1.3 with dep on GSL 2.2.1 --- .../g/GSL/GSL-2.2.1-intel-2016a.eb | 19 +++++++++++++ .../g/GSL/GSL-2.2.1-intel-2016b.eb | 19 +++++++++++++ .../s/STAMP/STAMP-1.3-intel-2016a.eb | 2 +- .../s/STAMP/STAMP-1.3-intel-2016b.eb | 27 +++++++++++++++++++ 4 files changed, 66 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016a.eb new file mode 100644 index 0000000000..6708b40368 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.2.1' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016b.eb new file mode 100644 index 0000000000..6a638ab6e5 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.2.1-intel-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.2.1' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb index 57a2608b75..4eb03dff01 100644 --- a/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://github.com/seqcode/stamp/archive/'] sources = ['v%(version)s.tar.gz'] -dependencies = [('GSL', '2.1')] +dependencies = [('GSL', '2.2.1')] start_dir = 'src' diff --git a/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016b.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016b.eb new file mode 100644 index 0000000000..51a70d8dc1 --- /dev/null +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'CmdCp' + +name = 'STAMP' +version = '1.3' + +homepage = 'http://www.benoslab.pitt.edu/stamp/' +description = """STAMP is a tool for characterizing similarities between transcription factor binding motifs""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/seqcode/stamp/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GSL', '2.2.1')] + +start_dir = 'src' + +cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp $LDFLAGS -lm -lgsl -lgslcblas")] + +files_to_copy = [(['stamp'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stamp'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From ec95fd74d053bfa649a12891bab58f28509889a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Sep 2016 16:37:12 +0200 Subject: [PATCH 562/701] add easyconfig Ghostscript-9.19-intel-2016b.eb, add easyconfig cairo-1.14.6-intel-2016b.eb, add easyconfig pixman-0.34.0-intel-2016b.eb --- .../c/cairo/cairo-1.14.6-intel-2016b.eb | 43 +++++++++++++++++++ .../Ghostscript-9.19-intel-2016b.eb | 29 +++++++++++++ .../p/pixman/pixman-0.34.0-intel-2016b.eb | 20 +++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb new file mode 100644 index 0000000000..54967b2ef7 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-intel-2016b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +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': '2016b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('freetype', '2.6.5'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('X11', '20160819'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb new file mode 100644 index 0000000000..8612f2848b --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.19' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +sources = ["ghostpdl-%(version)s.tar.bz2"] + +dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('freetype', '2.6.5'), + ('libjpeg-turbo', '1.5.0'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('cairo', '1.14.6'), + ('LibTIFF', '4.0.6'), +] + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb new file mode 100644 index 0000000000..ae4b777250 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-intel-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +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': '2016b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 68ce8ab99ce288d6a25fdcd831455dc284bb1248 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Sep 2016 18:35:09 +0200 Subject: [PATCH 563/701] add easyconfig pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb, add easyconfig spglib-python-1.9.5-intel-2016b-Python-2.7.12.eb --- ...ymatgen-4.3.2-intel-2016b-Python-2.7.12.eb | 26 +++++++++++++++++++ ...-python-1.9.5-intel-2016b-Python-2.7.12.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.5-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ff5f953560 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.3.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pymatgen' +version = '4.3.2' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('spglib-python', '1.9.5', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.5-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.5-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..7dd378ce55 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.5-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.9.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' -- GitLab From 82e76d737a14ade6e8cf18b269994fbe5f517fe5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Sep 2016 09:22:49 +0200 Subject: [PATCH 564/701] Fix PCRE issue: make SWIG have PCRE versionsuffix --- ....10-intel-2016b-Python-2.7.12-PCRE-8.39.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12-PCRE-8.39.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12-PCRE-8.39.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12-PCRE-8.39.eb new file mode 100644 index 0000000000..a1d01b931e --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12-PCRE-8.39.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.10' +versionsuffix = '-Python-%(pyver)s-PCRE-8.39' + +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': '2016b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PCRE', '8.39'), +] + +moduleclass = 'devel' -- GitLab From 3e38446dc0b0f8359a18ccb97fa47361ccbfb80b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Sep 2016 09:32:09 +0200 Subject: [PATCH 565/701] Drop unused easyconfig and fix SWIG/PLplot incompatiblity --- ...intel-2016b-Java-1.7.0_80-Python-2.7.12.eb | 2 +- .../SWIG-3.0.10-intel-2016b-Python-2.7.12.eb | 2 +- .../SWIG-3.0.8-intel-2016b-Python-2.7.12.eb | 20 ------------------- 3 files changed, 2 insertions(+), 22 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb index e8ab2cacc4..fb25f08bf9 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.6.1'), - ('SWIG', '3.0.10', '-Python-%(pyver)s'), + ('SWIG', '3.0.10', '-Python-%(pyver)s-PCRE-8.39'), ('libtool', '2.4.6'), ] diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb index 383771a5de..fed2dcb3c3 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.12'), - ('PCRE', '8.39'), + ('PCRE', '8.38'), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-2.7.12.eb deleted file mode 100644 index 00ac605f8c..0000000000 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,20 +0,0 @@ -name = 'SWIG' -version = '3.0.8' -versionsuffix = '-Python-%(pyver)s' - -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': '2016b'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.12'), - ('PCRE', '8.38'), -] - -moduleclass = 'devel' -- GitLab From 3eb67ce6de1d6732408ce0e7495ce1592ffcb153 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Sep 2016 09:33:13 +0200 Subject: [PATCH 566/701] Another unused easyconfig --- .../SWIG-3.0.8-intel-2016b-Python-3.5.2.eb | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-3.5.2.eb deleted file mode 100644 index 230fa8885d..0000000000 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-intel-2016b-Python-3.5.2.eb +++ /dev/null @@ -1,20 +0,0 @@ -name = 'SWIG' -version = '3.0.8' -versionsuffix = '-Python-%(pyver)s' - -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': '2016b'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '3.5.2'), - ('PCRE', '8.38'), -] - -moduleclass = 'devel' -- GitLab From 814fedbfabbe309c0019b59c5d7bee50129bf758 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 27 Sep 2016 15:20:01 +0200 Subject: [PATCH 567/701] Consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs --- easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb index 747a5dbe94..0f99148abf 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb index 434b6f02ff..76649c745f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb index 114b490972..dfad3c306d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb index 78e9122ea4..f82cf9fb58 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCCcore builddependencies = [('binutils', '2.27', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb index 6f774b05e4..34226edcc2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb @@ -16,7 +16,7 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.27', '', True)] -configopts = "--enable-cxx" +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 'files': ["bin/m4"], -- GitLab From 281140476033d730a3f42be6cafddbfebc35a2f7 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 27 Sep 2016 16:23:28 +0200 Subject: [PATCH 568/701] Add comment explaining why -fgnu89-inline is needed --- easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 2 ++ 40 files changed, 80 insertions(+) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb index 8398e40d06..54365e5c12 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.06'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb index b84761b602..41431f6ed6 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb index b4bb4c955d..91d64e5bd3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb index 5df1dda5a3..cb0daa392f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb index f406268a87..e59131c48f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb index 560606e07a..c9b8ae162c 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb index 00b1eb05a8..d52dd469f6 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb index a939e01023..5658dda837 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb index 64c98aad33..006446b9f0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb index 745063ebad..e7a4d305fe 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb index a95ac9f601..6e2de92ed5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb index 0f99148abf..ab63650383 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb index 5551b81d85..4a7f47d9bc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb index 02f06d5cfe..72fbf1541b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb index fa161623a1..83effb6682 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb index 76649c745f..d508b59ac7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb index dfad3c306d..702e859518 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb index f82cf9fb58..87ca206fb4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCCcore builddependencies = [('binutils', '2.27', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb index 34226edcc2..9a89ad1fbd 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.27', '', True)] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 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 index 134d181212..9fd3840472 100644 --- 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 @@ -13,6 +13,8 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb index 25f9aacace..222b4603e6 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 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 index 5ca90d16a7..8d48b94390 100644 --- 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 @@ -13,6 +13,8 @@ toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 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 index 4abe05a74f..4190871d6e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { 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 index f58173164e..6b8e25d1d4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb index 6a7048dcf1..414bbac849 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb index ef1614fe9a..e93393c961 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016.04'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb index ce563e7def..32fe2f7b78 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb index e7ea6f7b85..3d6737ba08 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb index aa806c1087..04ba474daf 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb index 304b160de5..ca3c0c7b6c 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb index 46c1b375cb..e8ed91309a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb index 0289e6c40e..a896f05992 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb index 857e1b9ffc..bd224278e8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb index a805266216..942e49510c 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb index 6746b4b3a4..dbdac66931 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb index 899804b18f..683e8274c8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb index 4472772492..2b9dd5a6b8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb index a7e7ddf81e..d339ed79b8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb index 104ad6a3bd..cda9d848b7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel-para', 'version': '2014.12'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 2bc8d9c022..159d8d0173 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -15,6 +15,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { -- GitLab From 1b6456ea7722e1283d2ea252ce5dec4aa266918b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 27 Sep 2016 16:43:27 +0200 Subject: [PATCH 569/701] add easyconfig PGDSpider-2.1.0.3-Java-1.7.0_80.eb --- .../PGDSpider-2.1.0.3-Java-1.7.0_80.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb new file mode 100644 index 0000000000..4071bc769a --- /dev/null +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock='Tarball' + +name = "PGDSpider" +version = "2.1.0.3" +versionsuffix = "-Java-%(javaver)s" + +homepage = 'http://cmpg.unibe.ch/software/PGDSpider/' +description = """An automated data conversion tool for connecting population genetics and genomics programs""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://cmpg.unibe.ch/software/PGDSpider/'] +sources = ['%(name)s_%(version)s.zip'] + +dependencies = [ + ('Java', '1.7.0_80', '', True), +] + +sanity_check_paths = { + 'files': ['PGDSpider2-cli.jar', 'PGDSpider2.jar'], + 'dirs': [], +} + +modloadmsg = """ +To execute GUI run: java -Xmx1024m -Xms512m -jar \\$EBROOTPGDSPIDER/PGDSpider2.jar +To execute CLI run: java -Xmx1024m -Xms512m -jar \\$EBROOTPGDSPIDER/PGDSpider2-cli.jar +Adjust memory according to your requirements""" + +moduleclass = 'bio' -- GitLab From ea14cfea8fca9d104909a9b4e1dce5316be93a49 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 27 Sep 2016 16:43:46 +0200 Subject: [PATCH 570/701] add easyconfig SelEstim-1.1.4-Linux-64bits.eb --- .../s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb diff --git a/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb new file mode 100644 index 0000000000..7b46114c2f --- /dev/null +++ b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'SelEstim' +version = '1.1.4' +versionsuffix = '-Linux-64bits' + +homepage = 'http://www1.montpellier.inra.fr/CBGP/software/selestim/index.html' +description = """SelEstim is aimed at distinguishing neutral from selected polymorphisms and estimate + the intensity of selection at the latter. The SelEstim model accounts explicitly for positive selection, + and it is assumed that all marker loci in the dataset are responding to selection, to some extent""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www1.montpellier.inra.fr/CBGP/software/selestim/files/'] +sources = ['%(name)s_%(version)s.zip'] + +postinstallcmds = [ + "rm -fr %(installdir)s/__MACOSX/ ", + "mv %(installdir)s/SelEstim_%(version)s/* %(installdir)s ", + "rm %(installdir)s/bin/SelEstim_1.1.4_OSX64bits ", + "rm %(installdir)s/bin/SelEstim_1.1.4_Linux32bits ", + "cd %(installdir)s/bin/ && ln -s SelEstim_%(version)s_Linux64bits SelEstim ", +] + +sanity_check_paths = { + 'files': ['bin/SelEstim_%(version)s_Linux64bits'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 5a532c11a3e8a425a4e2a3655df5e220666aa00c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 27 Sep 2016 17:02:42 +0200 Subject: [PATCH 571/701] Dummy worker easyconfig This is a weird easyconfig, ignore it please. It builds worker with system gcc and perl yet depends on the toolchain as a build dep. --- .../w/worker/worker-1.6.7-intel-2016b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb new file mode 100644 index 0000000000..f9fffe7804 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.7' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] + +tcname = 'intel' +tcver = '2016b' +builddependencies = [(tcname, tcver)] +versionsuffix = '-%s-%s' % (tcname, tcver) + +exts_defaultclass = 'PerlModule' + +exts_list = [ + ('Config::General', '2.61', { + 'source_tmpl': 'Config-General-2.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-1.636.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), +] + +modextrapaths = { + 'PERL5LIB': ['share/perl5', 'lib64/perl5'], +} + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (tcname, tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', +] + +moduleclass = 'tools' -- GitLab From 3b116182315c2b3a9af74978c01e9ef3a7dae42a Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 27 Sep 2016 23:05:52 +0200 Subject: [PATCH 572/701] style fix --- .../easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb index 7b46114c2f..7fd49e7b9f 100644 --- a/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb +++ b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb @@ -21,9 +21,9 @@ sources = ['%(name)s_%(version)s.zip'] postinstallcmds = [ "rm -fr %(installdir)s/__MACOSX/ ", - "mv %(installdir)s/SelEstim_%(version)s/* %(installdir)s ", - "rm %(installdir)s/bin/SelEstim_1.1.4_OSX64bits ", - "rm %(installdir)s/bin/SelEstim_1.1.4_Linux32bits ", + "mv %(installdir)s/SelEstim_%(version)s/* %(installdir)s ", + "rm %(installdir)s/bin/SelEstim_1.1.4_OSX64bits ", + "rm %(installdir)s/bin/SelEstim_1.1.4_Linux32bits ", "cd %(installdir)s/bin/ && ln -s SelEstim_%(version)s_Linux64bits SelEstim ", ] -- GitLab From fea54b2a6f04ef9b7f3662de1edf106895198ad6 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 28 Sep 2016 08:52:05 +0200 Subject: [PATCH 573/701] flex can be built in parallel --- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb | 2 -- 6 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index 155b9e6155..7890b40d70 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -19,6 +19,4 @@ dependencies = [ # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -parallel = 1 - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb index d1a9375e34..896d90dc34 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb @@ -19,6 +19,4 @@ dependencies = [ # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] -parallel = 1 - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index d5c3db995c..1c5de5599b 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -19,6 +19,4 @@ dependencies = [ # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] -parallel = 1 - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb index 2801060df2..2e2b6fd6cf 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb @@ -19,6 +19,4 @@ dependencies = [ # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', True)] -parallel = 1 - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb index a0f6f0c641..8f2ab256cd 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -19,6 +19,4 @@ dependencies = [ # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.27', '', True)] -parallel = 1 - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb index 239f478236..28fa3061c0 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb @@ -19,6 +19,4 @@ dependencies = [ # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.27', '', True)] -parallel = 1 - moduleclass = 'lang' -- GitLab From 064c17eae2b16d2d24c008de25aabe886851fb50 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Sep 2016 14:32:04 +0200 Subject: [PATCH 574/701] scikit-learn bump to 0.18 --- ...it-learn-0.18-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..cedad0e0ae --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 588edbbf43a8fac770fcb78d186a8412fe355471 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 29 Sep 2016 10:21:24 +0200 Subject: [PATCH 575/701] Add FDS/6.5.2 --- .../f/FDS/FDS-6.5.2-intel-2016b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb new file mode 100644 index 0000000000..477d5d84f2 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.5.2' + +homepage = 'https://pages.nist.gov/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': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['Git-r21.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 + +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] + +modextrapaths = {'PATH': 'FDS_Compilation'} + +sanity_check_paths = { + 'files': ['FDS_Compilation/fds'], + 'dirs': [], +} + +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + +moduleclass = 'phys' -- GitLab From 1a2c860d2a4566d0ac2d486941d5bd764101921d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 29 Sep 2016 12:25:11 +0200 Subject: [PATCH 576/701] use version template --- easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb index 102136d546..3a71d722f0 100644 --- a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb +++ b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb @@ -20,7 +20,7 @@ source_urls = ['http://kimura.univ-montp2.fr/PopPhyl/resources/tools/'] sources = ['%(namelower)s_%(version)s.zip'] sanity_check_paths = { - 'files': ['reads2snp_2.0.64.bin'], + 'files': ['reads2snp_%(version)s.64.bin'], 'dirs': [], } -- GitLab From ff5f258397cd90c7811c84d384a179650d1c93ec Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 29 Sep 2016 12:26:25 +0200 Subject: [PATCH 577/701] removed the chmod -x for the 32 bits version --- easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb index 3a71d722f0..506890dce2 100644 --- a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb +++ b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb @@ -28,7 +28,4 @@ modextrapaths = { 'PATH': "", # add the installation dir to PATH } -# disable exec permission for the provided 32 bits binary -postinstallcmds = ['chmod -x %(installdir)s/reads2snp_%(version)s.32.bin'] - moduleclass = 'bio' -- GitLab From c0689e183458a437e5b26fd910784e0ee11ce66e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 29 Sep 2016 14:57:41 +0200 Subject: [PATCH 578/701] ea-utils with foss2016a --- .../e/ea-utils/ea-utils-27a4809-foss-2016a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb new file mode 100644 index 0000000000..305396e578 --- /dev/null +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'ea-utils' +version = '27a4809' + +homepage = 'https://code.google.com/p/ea-utils/' +description = """Command-line tools for processing biological sequencing data. +Barcode demultiplexing, adapter trimming, etc. + +Primarily written to support an Illumina based pipeline - +but should work with any FASTQs.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/ExpressionAnalysis/%(name)s/tarball/master'] +sources = [SOURCE_TGZ] + +checksums = ['45eef4b040f83abe2c9f51d4a7d18271'] + +start_dir = 'clipper' + +prebuildopts = "sed -i 's/$(CFLAGS)/$(CFLAGS) $(LDFLAGS) -I./' Makefile && PREFIX=%(installdir)s " +buildopts = 'fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall' + +builddependencies = [ + ('Perl', '5.22.1'), +] + +dependencies = [ + ('GSL', '2.1'), +] + +files_to_copy = [(['fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', 'sam-stats', 'varcall', 'randomFQ', 'alc', 'determine-phred'], 'bin')] + + +sanity_check_paths = { + 'files': ['bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall'], + 'dirs': [] +} + +moduleclass = 'bio' \ No newline at end of file -- GitLab From d0574b31f92bcf81384204b230b747302f7fcfd2 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 29 Sep 2016 15:01:32 +0200 Subject: [PATCH 579/701] long lines --- .../e/ea-utils/ea-utils-27a4809-foss-2016a.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb index 305396e578..7cf3821ef3 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb @@ -31,11 +31,17 @@ dependencies = [ ('GSL', '2.1'), ] -files_to_copy = [(['fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', 'sam-stats', 'varcall', 'randomFQ', 'alc', 'determine-phred'], 'bin')] +files_to_copy = [([ + 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', + 'sam-stats', 'varcall', 'randomFQ', 'alc', 'determine-phred'], 'bin' +)] sanity_check_paths = { - 'files': ['bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall'], + 'files': [ + 'bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', + 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall' + ], 'dirs': [] } -- GitLab From 6f07b0f101826b36fbdcb3995f0157f42aef2efe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 30 Sep 2016 09:38:39 +0200 Subject: [PATCH 580/701] fix source URLs for Cython --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 3 ++- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb | 3 ++- easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb | 3 ++- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb | 3 ++- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 3 ++- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb | 3 ++- 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-foss-2015b.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 +- .../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-2015.06.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.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-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.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 +- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 3 ++- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 2 +- 59 files changed, 67 insertions(+), 59 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 1d651d49d1..f325e4238c 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 @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index 2247b6ef92..1ba18083e7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb index 74123d2915..e615c89354 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb @@ -66,7 +66,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb index 803575d935..7d445cd6ba 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb index 894b701f69..55f10df08f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 3d970938c9..017e1ecaae 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 @@ -67,7 +67,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index 8b5d70e944..276aa8a0f3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -66,7 +66,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 458773a19c..1837c2a90e 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 8847eb716a..9adcb16dd0 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 @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 8721ba5f0a..9f64cf9e32 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 feaf2e76ec..6c61e020b7 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 @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb index 7bff359058..c93dab2804 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 6bbc4316af..f07bce51db 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 b671309381..0b81650489 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 383cedbc17..0bca041c4c 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 ffaa43d1ef..a72f677c7d 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 b20ffd67fb..53cdae92ab 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 e087117a23..4cd83e24d0 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 04f049367b..0b9eaa28a2 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 f3c7ccd43d..31b3323fc1 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 65a7050c90..2608210a17 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 @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 caf683b0c8..4ffdd56f78 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 @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 a68ef18929..35bbb97553 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 @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 b36520e7e8..367298ed3a 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 3806ea6dd7..32d5421553 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 @@ -61,7 +61,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 e8290ac41a..ad8c5d8317 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 @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 577653d1f5..d2f51e3f22 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 @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 45b1ca6a64..648ac1994a 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 @@ -60,7 +60,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 33dce6f6ca..c0ac0d38b1 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 @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 0a01b973a0..513384d5b5 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 @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 f5d6db6b40..09835cdeb7 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 @@ -62,7 +62,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.17.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 bccfcbf0c2..95ff34f3f9 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.19.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.4.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 146417325f..d289934164 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 @@ -60,7 +60,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.19.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.4.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 a51d51c986..055543dc24 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 @@ -60,7 +60,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.19.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.4.1', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 16590efbbd..0409f54975 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 @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 c8491023d8..2a90fee410 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 @@ -66,7 +66,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 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 a7caba4fae..d975d85c2d 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 @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 dfe5979c7c..dca27371ed 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 @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 54121e1a6f..a7d56bba16 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 @@ -64,7 +64,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 012b08cef6..6b2fccea28 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 @@ -61,7 +61,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb index 21613bcfb7..2c98486b92 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb @@ -64,7 +64,7 @@ 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://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb index 9958308892..23449c0834 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb @@ -64,7 +64,7 @@ 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://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 f6e75ecf53..5ca1dda84e 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 @@ -64,7 +64,7 @@ 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://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 d693b53480..b636f6b2ef 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 @@ -64,7 +64,7 @@ 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://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb index 62fde498fb..82282d02d9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb @@ -64,7 +64,7 @@ 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://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 39cc28b030..987f0852f6 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 @@ -64,7 +64,7 @@ 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://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index fc6fced509..37abf12093 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -64,7 +64,7 @@ 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://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 09da0c6f20..7bdd55756a 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 @@ -64,7 +64,7 @@ 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://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 82f1c9fdc5..24081c5cf8 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 @@ -65,7 +65,7 @@ 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://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 9282981b3f..ae3c7ddc7a 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/'], }), ('Cython', '0.19.1', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('deap', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 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 98e26ec9ef..fc5033662d 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/'], }), ('Cython', '0.19.1', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('deap', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 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 b110143efd..f10e1b0d7d 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/'], }), ('Cython', '0.19.1', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('deap', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 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 4bc546cccb..1fe945390a 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/'], }), ('Cython', '0.19.1', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('deap', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 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 66630e9980..ba9c2f40b2 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 @@ -66,7 +66,7 @@ exts_list = [ 'checksums': ['ce61468d4c1263e3005737bbed2641f0'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 d93f95e46a..910cb21e5c 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 @@ -66,7 +66,7 @@ exts_list = [ 'checksums': ['ce61468d4c1263e3005737bbed2641f0'], }), ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.7.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 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 f8a3851092..8f08cf73e4 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 @@ -63,7 +63,8 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.22', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'source_tmpl': 'cython-%(version)s.tar.gz', }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index 40ab1396ff..825c8e6b10 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -66,7 +66,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.23.2', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index c0d918fab2..129c326cbb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -66,7 +66,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.23.4', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index bb39588cab..395e40515b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), ('Cython', '0.23.4', { - 'source_urls': ['http://www.cython.org/release/'], + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], }), ('six', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], -- GitLab From 9b05b21cbafe9536da04efdaee56b9a600fd2c83 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 30 Sep 2016 15:10:25 +0200 Subject: [PATCH 581/701] {data} [intel/2016b] PostgreSQL/9.6 --- ...tgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a1b0d0ba13 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.6.0' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.24.0'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' -- GitLab From 0b0b3d97ab4090fb03b4c76b3adbfdb6e493dd85 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 30 Sep 2016 17:16:39 +0200 Subject: [PATCH 582/701] {numlib} [intel/2016b] FGSL/1.10 --- .../f/FGSL/FGSL-1.10-intel-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb b/easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb new file mode 100644 index 0000000000..de3d855375 --- /dev/null +++ b/easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FGSL' +version = '1.1.0' + +homepage = 'https://www.lrz.de/services/software/mathematik/gsl/fortran/' +description = """FGSL: A Fortran interface to the GNU Scientific Library""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/reinh-bader/fgsl/archive/'] + +dependencies = [('GSL', '2.1')] + +builddependencies = [ + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), +] + +preconfigopts = 'autoreconf -fvi && ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['libfgsl.%s' % SHLIB_EXT, 'libfgsl.a'], + 'dirs': ['include/fgsl', 'lib/pkgconfig'] +} + +moduleclass = 'numlib' -- GitLab From eb5af1122d14dc56039aec45bcafea5fb2f89c65 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 30 Sep 2016 17:25:21 +0200 Subject: [PATCH 583/701] Correct sanity check --- easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb b/easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb index de3d855375..e06458da7e 100644 --- a/easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb @@ -23,7 +23,7 @@ preconfigopts = 'autoreconf -fvi && ' runtest = 'check' sanity_check_paths = { - 'files': ['libfgsl.%s' % SHLIB_EXT, 'libfgsl.a'], + 'files': ['lib/libfgsl.%s' % SHLIB_EXT, 'lib/libfgsl.a'], 'dirs': ['include/fgsl', 'lib/pkgconfig'] } -- GitLab From edd7c3ef28439923c962b9a017e7e7711b7b5e3c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 30 Sep 2016 17:26:18 +0200 Subject: [PATCH 584/701] Correct name --- .../FGSL/{FGSL-1.10-intel-2016b.eb => FGSL-1.1.0-intel-2016b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/FGSL/{FGSL-1.10-intel-2016b.eb => FGSL-1.1.0-intel-2016b.eb} (100%) diff --git a/easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb b/easybuild/easyconfigs/f/FGSL/FGSL-1.1.0-intel-2016b.eb similarity index 100% rename from easybuild/easyconfigs/f/FGSL/FGSL-1.10-intel-2016b.eb rename to easybuild/easyconfigs/f/FGSL/FGSL-1.1.0-intel-2016b.eb -- GitLab From 4220a0392301dfaae03b9249455b90a795832e24 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 30 Sep 2016 17:28:50 +0200 Subject: [PATCH 585/701] {vis} [intel/2016b] ImageMagick/7.0.3-1 --- .../ImageMagick-7.0.3-1-intel-2016b.eb | 41 +++++++++++++++++++ .../l/LittleCMS/LittleCMS-2.8-intel-2016b.eb | 23 +++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2016b.eb diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb new file mode 100644 index 0000000000..f3c4211e84 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.3-1' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://www.imagemagick.org/download'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('X11', '20160819'), + ('Ghostscript', '9.19'), + ('JasPer', '1.900.1'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), + ('LittleCMS', '2.8'), +] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2016b.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2016b.eb new file mode 100644 index 0000000000..738095618f --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.8' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] + +dependencies = [('libjpeg-turbo', '1.5.0')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' -- GitLab From 44bd3c4bb464c2a789e2402ea8738546a73fb3af Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 4 Oct 2016 14:44:44 +0200 Subject: [PATCH 586/701] patch for failing pdflatex tests --- ... Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb} | 5 ++++- ...> Sphinx-1.4.6-foss-2016a-Python-3.5.1.eb} | 5 ++++- .../Sphinx-1.4.6-pdflatex_failing_tests.patch | 20 +++++++++++++++++++ 3 files changed, 28 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/Sphinx/{Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb => Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb} (97%) rename easybuild/easyconfigs/s/Sphinx/{Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb => Sphinx-1.4.6-foss-2016a-Python-3.5.1.eb} (96%) create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-pdflatex_failing_tests.patch diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb similarity index 97% rename from easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb index edf98e8d1e..864c3dcd54 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'Sphinx' -version = '1.4.5' +version = '1.4.6' versionsuffix = '-Python-%(pyver)s' homepage = 'http://sphinx.pocoo.org/' @@ -21,6 +21,9 @@ dependencies = [ ('requests', '2.10.0', versionsuffix), ] +patches = [ + 'failing_tests.patch' +] exts_list = [ ('imagesize', '0.7.1', { diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-3.5.1.eb similarity index 96% rename from easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb rename to easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-3.5.1.eb index f608175b73..b334e2de65 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.5-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-3.5.1.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'Sphinx' -version = '1.4.5' +version = '1.4.6' versionsuffix = '-Python-%(pyver)s' homepage = 'http://sphinx.pocoo.org/' @@ -21,6 +21,9 @@ dependencies = [ ('requests', '2.10.0', versionsuffix), ] +patches = [ + '%(name)s-%(version)s-pdflatex_failing_tests.patch' +] exts_list = [ ('imagesize', '0.7.1', { diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-pdflatex_failing_tests.patch b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-pdflatex_failing_tests.patch new file mode 100644 index 0000000000..437e040640 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-pdflatex_failing_tests.patch @@ -0,0 +1,20 @@ +pdflatex and latex tests fail on systems that have older versions installed +Author: Ruben van Dijk (University of Groningen) +--- Makefile.orig 2016-10-04 14:15:46.000000000 +0200 ++++ Makefile 2016-10-04 14:37:19.000000000 +0200 +@@ -64,8 +64,14 @@ + reindent: + @$(PYTHON) utils/reindent.py -r -n . + ++# Failing tests, py35 was already excluded. ++DONT_TEST = -I py35 \ ++ -I latex \ ++ -I typing_test_data \ ++ -I ext_math ++ + test: +- @cd tests; $(PYTHON) run.py -I py35 -d -m '^[tT]est' $(TEST) ++ @cd tests; $(PYTHON) run.py $(DONT_TEST) -d #-m '^[tT]est' $(TEST) + + test-async: + @cd tests; $(PYTHON) run.py -d -m '^[tT]est' $(TEST) -- GitLab From 46d4707017c7efaa4e5bd86e7088824c9e930b2d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 4 Oct 2016 14:46:33 +0200 Subject: [PATCH 587/701] rename patch in sphinx-2.7.11 --- .../s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb index 864c3dcd54..8099523d58 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ ] patches = [ - 'failing_tests.patch' + '%(name)s-%(version)s-pdflatex_failing_tests.patch' ] exts_list = [ -- GitLab From 80d96d442bdcffabcb8505222851804259edef20 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 4 Oct 2016 14:47:06 +0200 Subject: [PATCH 588/701] omit newline --- .../p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb index d1cd521edb..85869f21ea 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-3.5.1.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '3.5.1'), ] -- GitLab From 2baffdc4d76cffebaa7d44d6ade4b482354133aa Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 5 Oct 2016 11:51:29 +0800 Subject: [PATCH 589/701] add easyconfig Elk-4.0.15-intel-2016.01.eb --- .../e/Elk/Elk-4.0.15-intel-2016.01.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016.01.eb diff --git a/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016.01.eb b/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016.01.eb new file mode 100644 index 0000000000..c217d02ed8 --- /dev/null +++ b/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016.01.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'Elk' +version = '4.0.15' + +homepage = 'http://elk.sourceforge.net/' +description = """An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with +many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the +EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that +new developments in the field of density functional theory (DFT) can be added quickly and reliably. +""" + +toolchain = {'name': 'intel', 'version': '2016.01'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TGZ] +source_urls = [SOURCEFORGE_SOURCE] + +checksums = [ + '760623faf5aab9b1f49488edbaae65fb', # elk-4.0.15.tgz +] + +dependencies = [ + ('libxc', '2.2.3'), +] + + +# make.inc file is generated interactively by "setup" command, creating it here +prebuildopts = 'echo "F90_OPTS = $FFLAGS" > make.inc && ' +prebuildopts += 'echo "F77_OPTS = $FFLAGS" >> make.inc && ' +prebuildopts += 'echo "LIB_LPK = $LIBLAPACK" >> make.inc && ' +prebuildopts += 'echo "LIB_libxc = $EBROOTLIBXC/lib/libxcf90.a $EBROOTLIBXC/lib/libxc.a" >> make.inc && ' +prebuildopts += 'echo "SRC_libxc = libxc_funcs.f90 libxc.f90 libxcifc.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_FFT = zfftifc_fftw.f90" >> make.inc && ' + +buildopts = 'all' + +parallel = 1 + +files_to_copy = [(['src/elk', 'src/spacegroup/spacegroup', 'src/eos/eos'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/elk', 'bin/spacegroup', 'bin/eos'], + 'dirs': [] +} + +moduleclass = 'phys' -- GitLab From 2b5c7943458bef82bc5c1f682b0c1b0dc9981b3a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 5 Oct 2016 17:14:42 +0800 Subject: [PATCH 590/701] switch toolchain to 2016b --- .../{Elk-4.0.15-intel-2016.01.eb => Elk-4.0.15-intel-2016b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/e/Elk/{Elk-4.0.15-intel-2016.01.eb => Elk-4.0.15-intel-2016b.eb} (96%) diff --git a/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016.01.eb b/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016b.eb similarity index 96% rename from easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016.01.eb rename to easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016b.eb index c217d02ed8..e2db42a61e 100644 --- a/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016.01.eb +++ b/easybuild/easyconfigs/e/Elk/Elk-4.0.15-intel-2016b.eb @@ -10,7 +10,7 @@ EXCITING EU Research and Training Network, the code is designed to be as simple new developments in the field of density functional theory (DFT) can be added quickly and reliably. """ -toolchain = {'name': 'intel', 'version': '2016.01'} +toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} sources = [SOURCELOWER_TGZ] -- GitLab From e4401640e583f6e62a39583e22b190c433e9f467 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2016 10:43:12 +0200 Subject: [PATCH 591/701] add easyconfig awscli-1.11.1-intel-2016b-Python-2.7.12.eb --- ...awscli-1.11.1-intel-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ce1d7a97a9 --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-1.11.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'awscli' +version = '1.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'tools' -- GitLab From b734eda73803b6f761787341790aef8c0709174a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 7 Oct 2016 10:48:28 +0800 Subject: [PATCH 592/701] add easyconfig QuantumESPRESSO-6.0-intel-2016b.eb --- .../QuantumESPRESSO-6.0-intel-2016b.eb | 55 ++++++++++++++ .../QuantumESPRESSO-6.0_yambo-fixes.patch | 71 +++++++++++++++++++ 2 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0_yambo-fixes.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb new file mode 100644 index 0000000000..a7b85783a2 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb @@ -0,0 +1,55 @@ +name = 'QuantumESPRESSO' +version = '6.0' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'qe-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'qe-gipaw-6.0.tar.gz', + # must be downloaded manually from + # http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=%2F%2Acheckout%2A%2Ftags%2FQE-5.2.1%2Fespresso%2Farchive%2Fplumed-1.3-qe.tar.gz&revision=11758 + # gets updated without changes to filename, cfr. http://qe-forge.org/pipermail/q-e-commits/2015-June/007359.html + # 'plumed-1.3-qe-r11758.tar.gz', + 'want-2.5.1-base.tar.gz', + 'yambo-3.4.2.tgz', +] +missing_sources = [ + 'sax-2.0.3.tar.gz', # nowhere to be found +] +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/224/1044/', # qe-6.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/208/932/', # yambo-3.4.2.tgz +] + +patches = [ + 'QuantumESPRESSO-%(version)s_yambo-fixes.patch', +] + +# source checksums +checksums = [ + 'e42aeeffadf7951542d8561a6b4a3390', # qe-6.0.tar.gz + 'a1e9611b9a82941c23426028d112186e', # wannier90-1.2.tar.gz + 'b11a8b75109eb58fd97a1c6f7cf20e31', # qe-gipaw-6.0.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + 'f0820a0f42dfc81ce3811af647bed777', # yambo-3.4.2.tgz +] + +# add plumed and uncomment the lines in sources and checksums if the package is downloaded manually +buildopts = 'all w90 gipaw want yambo xspectra' # plumed + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0_yambo-fixes.patch new file mode 100644 index 0000000000..8f94d88eb2 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0_yambo-fixes.patch @@ -0,0 +1,71 @@ +* make sure -nofor_main is also used when $FC is defined as mpif90 for yambo +* fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output +* force ifort mangling in yambo's netcdf +author: Kenneth Hoste (HPC-UGent), adapted to qe-6.0 and yambo-3.4.2 by Miguel Dias Costa (National University of Singapore) +--- qe-6.0/yambo-3.4.2/configure.orig 2016-05-26 16:18:16.177156000 +0800 ++++ qe-6.0/yambo-3.4.2/configure 2016-05-26 16:20:31.929218336 +0800 +@@ -6238,7 +6238,7 @@ + ;; + *g95*) + ;; +- *ifort*) ++ *ifort*|*mpif90*) + $FC -v >& ver_ + VER_8=`grep 8. ver_ | wc -l` + VER_9=`grep 9. ver_ | wc -l` +@@ -6321,7 +6321,7 @@ + FCMFLAG="" + OMPFLAGS="-fopenmp" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* |*14* | *15* ) +@@ -6365,7 +6365,7 @@ + UFFLAGS="-g -O0 -fno-second-underscore" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6413,7 +6413,7 @@ + UFFLAGS="-g -O0 -w" + OMPFLAGS="-openmp" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6472,7 +6472,7 @@ + UFFLAGS="-g -O0 -w -tpp2" + OMPFLAGS="-openmp" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* |*14* |*15* ) +@@ -7651,7 +7651,7 @@ + + if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then + eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} +- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 >&5 ++ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 >&5 + if test -s conftest.er2 ; then + if ! test -n "`grep successful conftest.er2`" ; then + acx_F90_ok=no ; +--- qe-6.0/yambo-3.4.2/lib/netcdf/Makefile.loc.orig 2016-06-02 17:29:53.816844000 +0800 ++++ qe-6.0/yambo-3.4.2/lib/netcdf/Makefile.loc 2016-06-02 17:30:45.579476000 +0800 +@@ -40,7 +40,7 @@ + FC="$(f90)" \ + FCFLAGS="$(f77flags)" \ + FFLAGS="$(f77flags)" \ +- CPPFLAGS="$(netcdf_aux)" \ ++ CPPFLAGS="$(netcdf_aux) -DpgiFortran" \ + F90="$(f90)" \ + F77="$(f77)" \ + INSTALL_DIR="$(INSTALL_DIR)" ); \ -- GitLab From 26862e351845e235b7a32bda8ba0c609d919d984 Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 7 Oct 2016 10:36:20 +0200 Subject: [PATCH 593/701] bump version to 8.2.9 --- .../RAxML-8.2.9-foss-2016a-hybrid-avx2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.9-foss-2016a-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.9-foss-2016a-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.9-foss-2016a-hybrid-avx2.eb new file mode 100644 index 0000000000..db82fd5e9a --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.9-foss-2016a-hybrid-avx2.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.9' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-HYBRID-AVX2"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e2c01b21f66ae629e9c30cd5c97426b8cec795a6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 7 Oct 2016 15:42:53 +0200 Subject: [PATCH 594/701] add easyconfig Mathematica-11.0.1.eb --- .../m/Mathematica/Mathematica-11.0.1.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb new file mode 100644 index 0000000000..6a3a3e02ee --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '11.0.1' + +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_%(version)s_LINUX.sh'] + +license_server = 'license.example.com' + +moduleclass = 'math' -- GitLab From 6bef0682d23a57e54ef6814f92a480e1a478a1e8 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 7 Oct 2016 15:54:14 +0200 Subject: [PATCH 595/701] working patch --- .../Sphinx-1.4.6-pdflatex_failing_tests.patch | 20 ------------------- ... Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb} | 7 ++----- ...> Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb} | 7 ++----- .../Sphinx-1.4.8-pdflatex_failing_tests.patch | 20 +++++++++++++++++++ 4 files changed, 24 insertions(+), 30 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-pdflatex_failing_tests.patch rename easybuild/easyconfigs/s/Sphinx/{Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb => Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb} (96%) rename easybuild/easyconfigs/s/Sphinx/{Sphinx-1.4.6-foss-2016a-Python-3.5.1.eb => Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb} (96%) create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-pdflatex_failing_tests.patch diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-pdflatex_failing_tests.patch b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-pdflatex_failing_tests.patch deleted file mode 100644 index 437e040640..0000000000 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-pdflatex_failing_tests.patch +++ /dev/null @@ -1,20 +0,0 @@ -pdflatex and latex tests fail on systems that have older versions installed -Author: Ruben van Dijk (University of Groningen) ---- Makefile.orig 2016-10-04 14:15:46.000000000 +0200 -+++ Makefile 2016-10-04 14:37:19.000000000 +0200 -@@ -64,8 +64,14 @@ - reindent: - @$(PYTHON) utils/reindent.py -r -n . - -+# Failing tests, py35 was already excluded. -+DONT_TEST = -I py35 \ -+ -I latex \ -+ -I typing_test_data \ -+ -I ext_math -+ - test: -- @cd tests; $(PYTHON) run.py -I py35 -d -m '^[tT]est' $(TEST) -+ @cd tests; $(PYTHON) run.py $(DONT_TEST) -d #-m '^[tT]est' $(TEST) - - test-async: - @cd tests; $(PYTHON) run.py -d -m '^[tT]est' $(TEST) diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb similarity index 96% rename from easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb index 8099523d58..249a32fcb8 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'Sphinx' -version = '1.4.6' +version = '1.4.8' versionsuffix = '-Python-%(pyver)s' homepage = 'http://sphinx.pocoo.org/' @@ -21,10 +21,6 @@ dependencies = [ ('requests', '2.10.0', versionsuffix), ] -patches = [ - '%(name)s-%(version)s-pdflatex_failing_tests.patch' -] - exts_list = [ ('imagesize', '0.7.1', { 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], @@ -51,6 +47,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' %version], }), # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work ('sphinx_rtd_theme', '0.1.10a0', { diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb similarity index 96% rename from easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-3.5.1.eb rename to easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb index b334e2de65..90efc667c6 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.6-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'Sphinx' -version = '1.4.6' +version = '1.4.8' versionsuffix = '-Python-%(pyver)s' homepage = 'http://sphinx.pocoo.org/' @@ -21,10 +21,6 @@ dependencies = [ ('requests', '2.10.0', versionsuffix), ] -patches = [ - '%(name)s-%(version)s-pdflatex_failing_tests.patch' -] - exts_list = [ ('imagesize', '0.7.1', { 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], @@ -51,6 +47,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' %version], }), # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work ('sphinx_rtd_theme', '0.1.10a0', { diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-pdflatex_failing_tests.patch b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-pdflatex_failing_tests.patch new file mode 100644 index 0000000000..44705787c3 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-pdflatex_failing_tests.patch @@ -0,0 +1,20 @@ +pdflatex and latex tests fail on systems that have older versions installed +Author: Ruben van Dijk (University of Groningen) +--- Sphinx-1.4.8/Makefile 2016-10-05 11:05:34.000000000 +0200 ++++ Sphinx-1.4.8/Makefile 2016-10-05 11:11:05.000000000 +0200 +@@ -67,8 +67,14 @@ + reindent: + @$(PYTHON) utils/reindent.py -r -n . + ++# Failing tests, py35 was already excluded. ++DONT_TEST = -I py35 \ ++ -I latex \ ++ -I typing_test_data \ ++ -I ext_math ++ + test: +- @cd tests; $(PYTHON) run.py -I py35 -d -m '^[tT]est' $(TEST) ++ @cd tests; $(PYTHON) run.py $(DONT_TEST) -d #-m '^[tT]est' $(TEST) + + test-async: + @cd tests; $(PYTHON) run.py -d -m '^[tT]est' $(TEST) -- GitLab From 402b7e4b38b88d3478a3ea845bd645e6a9485112 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 7 Oct 2016 15:56:55 +0200 Subject: [PATCH 596/701] Sphinx version update --- .../o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb index 8ecf00679f..d30d6266ab 100644 --- a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ dependencies = [ ('Cython', '0.24.1', versionsuffix), ('wheel', '0.29.0', versionsuffix), ('IPython', '5.0.0', versionsuffix), - ('Sphinx', '1.4.5', versionsuffix) + ('Sphinx', '1.4.8', versionsuffix) ] options = {'modulename': 'obitools'} -- GitLab From 2c50629a3696305720e09f00767ea52202a43fac Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 7 Oct 2016 16:09:20 +0200 Subject: [PATCH 597/701] OSU-micro 5.3.2 with foss --- .../OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb new file mode 100644 index 0000000000..1bc3f774aa --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.3.2' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC=$MPICC CXX=$MPICC' + +benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': benchmark_dirs, +} + +moduleclass = 'perf' -- GitLab From c067ea08def05b1d026da1f8aabc94ea9377487d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 7 Oct 2016 16:13:12 +0200 Subject: [PATCH 598/701] IMB-4.1 with foss --- .../easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb new file mode 100644 index 0000000000..7c82e8b734 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """ +The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && cd src &&' +buildopts = '-f make_mpich' + +patches = ['IMB-make_mpich.patch'] + +parallel = 1 + +files_to_copy = [ +(['src/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], 'bin'), +(['doc/IMB_Users_Guide.pdf'],'doc'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], + 'dirs': ['bin','doc'] +} + +moduleclass = 'tools' \ No newline at end of file -- GitLab From 4294702f82c0baba360d72e93468b8bb1fce92a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Oct 2016 16:18:03 +0200 Subject: [PATCH 599/701] add easyconfig CMake-3.6.2-intel-2016b.eb --- .../c/CMake/CMake-3.6.2-intel-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb new file mode 100644 index 0000000000..b6e496837c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.2' + +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': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # 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', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 88ab1b465f8e97758b27d268b161036b6f3a9f01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Oct 2016 16:57:58 +0200 Subject: [PATCH 600/701] add easyconfig SUNDIALS-2.7.0-intel-2016b.eb --- .../s/SUNDIALS/SUNDIALS-2.7.0-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-intel-2016b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-intel-2016b.eb new file mode 100644 index 0000000000..dc435288bd --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '2.7.0' + +homepage = 'http://computation.llnl.gov/projects/sundials' +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['http://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.6.2')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in solvers] + ['include/%s' % s for s in solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' -- GitLab From 002b73a00b5c7913f61331fb6c31bf570ceb1ff8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Oct 2016 18:56:52 +0200 Subject: [PATCH 601/701] add easyconfig Cantera-2.2.1-intel-2016b-Python-2.7.12.eb --- ...Cantera-2.2.1-intel-2016b-Python-2.7.12.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..d95d3fc7c6 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,36 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('Boost', '1.61.0', versionsuffix), + ('SUNDIALS', '2.7.0'), +] +builddependencies = [('SCons', '2.5.0', versionsuffix)] + +buildopts = 'CC="$CC" CXX="$CXX" env=all blas_lapack_libs=mkl_rt blas_lapack_dir=$BLAS_LAPACK_LIB_DIR' +buildopts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +#runtest = 'test' +prefix_arg = 'prefix=' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/mixmaster'], + 'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('python', "-c 'import cantera'")] + +moduleclass = 'chem' -- GitLab From e4306133240ddc09fe9e947ac01166578265675b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 10 Oct 2016 09:33:28 +0200 Subject: [PATCH 602/701] Make Bison a builddependency rather than a dependency Also add checksum --- .../easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb | 8 +++++--- .../easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 13 ++++++++----- .../easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb | 13 ++++++++----- .../easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 13 ++++++++----- .../easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb | 13 ++++++++----- .../easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb | 13 ++++++++----- .../easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb | 13 ++++++++----- .../easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb | 8 +++++--- .../easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb | 8 +++++--- .../easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb | 8 +++++--- .../easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb | 8 +++++--- .../easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb | 8 +++++--- .../easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb | 8 +++++--- .../easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb | 8 +++++--- easybuild/easyconfigs/f/flex/flex-2.6.0.eb | 8 +++++--- 15 files changed, 93 insertions(+), 57 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb index 9a286850a4..96c99f1d3c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCC-4.9.2.eb @@ -11,9 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index 7890b40d70..b7b82f9197 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -11,12 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.25', '', True), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb index 896d90dc34..73279c6d88 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb @@ -11,12 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.25', '', True), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index 1c5de5599b..954dea0d03 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -11,12 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.26', '', True), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb index 2e2b6fd6cf..ee9b4ed94d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb @@ -11,12 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.26', '', True), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb index 8f2ab256cd..51d6c9f7b6 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -11,12 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb index 28fa3061c0..43cfdfac42 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb @@ -11,12 +11,15 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb index 621cdb0aaf..5c0eb6b59d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2015a.eb @@ -11,9 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb index 5969d1e4b9..415a80ac04 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016a.eb @@ -11,9 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb index d24b602e70..626ebe5d46 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb @@ -11,9 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb index e6510e7ef7..3d60cee674 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-gimkl-2.11.5.eb @@ -11,9 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb index 59f659121c..098c6168e7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2015b.eb @@ -11,9 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb index ee500a048e..da18a62238 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016a.eb @@ -11,9 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb index acc1431c3f..1dc06e55c1 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb @@ -11,9 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb index 08a404a4b8..853b81ad96 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb @@ -11,9 +11,11 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -dependencies = [ - ('Bison', '3.0.4'), - ('M4', '1.4.17') +checksums = [ + '5724bcffed4ebe39e9b55a9be80859ec', # flex-2.6.0.tar.gz ] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' -- GitLab From 5b2e5eef7ad4302113f4069119ccc75c41bbc44c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Oct 2016 10:01:09 +0200 Subject: [PATCH 603/701] Add sanity command to Mathematica --- easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb index 6a3a3e02ee..624287d31c 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb @@ -11,4 +11,6 @@ sources = ['Mathematica_%(version)s_LINUX.sh'] license_server = 'license.example.com' +sanity_check_commands = [('mathematica', '--help')] + moduleclass = 'math' -- GitLab From 1a79725d94e28e3722b54b3325f12b7a4f9da43f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Oct 2016 10:22:57 +0200 Subject: [PATCH 604/701] Use sanity command that doesn't require X --- easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb index 624287d31c..2afcde5570 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb @@ -11,6 +11,6 @@ sources = ['Mathematica_%(version)s_LINUX.sh'] license_server = 'license.example.com' -sanity_check_commands = [('mathematica', '--help')] +sanity_check_commands = [('mathematica', '--version')] moduleclass = 'math' -- GitLab From ad597adc4c819f12008afa8961f063db081c8d0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Oct 2016 10:45:10 +0200 Subject: [PATCH 605/701] add missing easyconfig for SCons build dep --- .../SCons-2.5.0-intel-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.5.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..87b4206755 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' -- GitLab From 19600a8644c1836d4d0f8970112796f1ca5ffadc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 10 Oct 2016 11:39:27 +0200 Subject: [PATCH 606/701] {math}[binary] MCR R2016a (REVIEW) --- easybuild/easyconfigs/m/MCR/MCR-R2016a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2016a.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb new file mode 100644 index 0000000000..7314d95a8c --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2016a' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_92')] + +moduleclass = 'math' -- GitLab From 0a014212513282bd90cce5fed9eb5d22366dd1a0 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 10 Oct 2016 11:53:15 +0200 Subject: [PATCH 607/701] requested changes --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 12 +++++------- easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch | 11 +++++++++++ 2 files changed, 16 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index 7c82e8b734..f47f929afb 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -13,21 +13,19 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = ['%(name)s_%(version)s.tgz'] source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] -prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && cd src &&' +start_dir = 'src' +prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' buildopts = '-f make_mpich' -patches = ['IMB-make_mpich.patch'] +patches = ['IMB-%(version)s_make_mpich.patch'] parallel = 1 -files_to_copy = [ -(['src/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], 'bin'), -(['doc/IMB_Users_Guide.pdf'],'doc'), -] +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], 'dirs': ['bin','doc'] } -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch b/easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch new file mode 100644 index 0000000000..6805a1bc3c --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch @@ -0,0 +1,11 @@ +Prevent: Variable MPI_HOME="" does not seem to contain a valid mpicc. +Author: Fokke Dijkstra (University of Groningen) +--- src/make_mpich 2015-02-16 13:31:11.838082386 +0100 ++++ src/make_mpich 2015-02-16 13:40:19.000844455 +0100 +@@ -1,5 +1,5 @@ + # Enter root directory of mpich install +-MPI_HOME= ++#MPI_HOME= + + MPICC=$(shell find ${MPI_HOME} -name mpicc -print) + -- GitLab From b1eb59353a12fd8be5aaa1db252e2537f92a033b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 10 Oct 2016 12:06:09 +0200 Subject: [PATCH 608/701] double quotes --- .../OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb index 1bc3f774aa..d25cf1b3ab 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC=$MPICC CXX=$MPICC' +configopts = 'CC="$MPICC" CXX="$MPICC"' benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] modextrapaths = {'PATH': benchmark_dirs} -- GitLab From b1e01ba7486d80d4d860df1af00d6172ef7d0c2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2016 11:23:03 +0200 Subject: [PATCH 609/701] add easyconfig scikit-learn-0.18-intel-2016b-Python-3.5.2.eb, add easyconfig matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb --- ...tplotlib-1.5.1-intel-2016b-Python-3.5.2.eb | 45 +++++++++++++++++++ ...kit-learn-0.18-intel-2016b-Python-3.5.2.eb | 30 +++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..fe6afff731 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('freetype', '2.6.5'), + ('libpng', '1.6.24'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], + }), +] + +# 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': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..a4cbd22622 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('matplotlib', '1.5.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 800362e6f83be842ef18510079e90a9d3943817f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2016 11:37:50 +0200 Subject: [PATCH 610/701] add easyconfig Keras-1.1.0-intel-2016b-Python-3.5.2.eb --- .../Keras-1.1.0-intel-2016b-Python-3.5.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..503271be94 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-1.1.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Keras' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('Theano', '0.8.2', versionsuffix), + ('h5py', '2.6.0', '%(versionsuffix)s-HDF5-1.8.17'), + ('PyYAML', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From aee0cecafa3c1d21ec03a9ec2fc1802fb663919c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 11 Oct 2016 11:47:11 +0200 Subject: [PATCH 611/701] {vis}[foss/2016b] X11/20160819 - libz and bzip2 deps added (REVIEW) --- .../fontconfig-2.12.1-foss-2016b.eb | 22 +++ .../f/freetype/freetype-2.6.5-foss-2016b.eb | 26 ++++ .../l/libpng/libpng-1.6.24-foss-2016b.eb | 26 ++++ .../pkg-config-0.29.1-foss-2016b.eb | 27 ++++ .../x/X11/X11-20160819-foss-2016b.eb | 131 ++++++++++++++++++ .../x/X11/X11-20160819-intel-2016b.eb | 2 + 6 files changed, 234 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.24-foss-2016b.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2016b.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2016b.eb new file mode 100644 index 0000000000..be4b439455 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-foss-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' + +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': 'foss', 'version': '2016b'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', '2.6.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb new file mode 100644 index 0000000000..9156052c8f --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb @@ -0,0 +1,26 @@ +name = 'freetype' +version = '2.6.5' + +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': 'foss', 'version': '2016b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libpng', '1.6.24'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.24-foss-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-foss-2016b.eb new file mode 100644 index 0000000000..9f690e65b2 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.24' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016b.eb new file mode 100644 index 0000000000..7e76d64603 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +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).""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb new file mode 100644 index 0000000000..c44e65c206 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb @@ -0,0 +1,131 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20160819' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), +] +dependencies = [ + ('freetype', '2.6.5'), + ('fontconfig', '2.12.1'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.0', { + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.3', common_specs), + ('bigreqsproto', '1.1.2', common_specs), + ('compositeproto', '0.4.2', common_specs), + ('damageproto', '1.2.1', common_specs), + ('dmxproto', '2.3.1', common_specs), + ('dri2proto', '2.8', common_specs), + ('dri3proto', '1.0', common_specs), + ('fixesproto', '5.0', common_specs), + ('fontsproto', '2.1.3', common_specs), + ('glproto', '1.4.17', common_specs), + ('inputproto', '2.3.1', common_specs), + ('kbproto', '1.0.7', common_specs), + ('presentproto', '1.0', common_specs), + ('randrproto', '1.5.0', common_specs), + ('recordproto', '1.14.2', common_specs), + ('renderproto', '0.11', common_specs), + ('resourceproto', '1.2.0', common_specs), + ('scrnsaverproto', '1.2.2', common_specs), + ('videoproto', '2.3.3', common_specs), + ('xcmiscproto', '1.2.2', common_specs), + ('xextproto', '7.3.0', common_specs), + ('xf86bigfontproto', '1.2.0', common_specs), + ('xf86dgaproto', '2.1', common_specs), + ('xf86driproto', '2.1.1', common_specs), + ('xf86vidmodeproto', '2.3.1', common_specs), + ('xineramaproto', '1.2.1', common_specs), + ('xproto', '7.0.28', common_specs), + ('libXau', '1.0.8', common_specs), + ('libXdmcp', '1.1.2', common_specs), + ('xcb-proto', '1.11', common_specs), + ('libxcb', '1.11.1', common_specs), + ('xtrans', '1.3.5', common_specs), + ('libxkbcommon', '0.6.1', { + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.3', common_specs), + ('libXext', '1.3.3', common_specs), + ('libFS', '1.0.7', common_specs), + ('libICE', '1.0.9', common_specs), + ('libSM', '1.2.2', common_specs), + ('libXScrnSaver', '1.2.2', common_specs), + ('libXt', '1.1.5', common_specs), + ('libXmu', '1.1.2', common_specs), + ('libXpm', '3.5.11', common_specs), + ('libXaw', '1.0.13', common_specs), + ('libXfixes', '5.0.2', common_specs), + ('libXcomposite', '0.4.4', common_specs), + ('libXrender', '0.9.9', common_specs), + ('libXcursor', '1.1.14', common_specs), + ('libXdamage', '1.1.4', common_specs), + ('libfontenc', '1.1.3', common_specs), + ('libXfont', '1.5.1', common_specs), + ('libXft', '2.3.2', common_specs), + ('libXi', '1.7.6', common_specs), + ('libXinerama', '1.1.3', common_specs), + ('libXrandr', '1.5.0', common_specs), + ('libXres', '1.0.7', common_specs), + ('libXtst', '1.2.2', common_specs), + ('libXv', '1.0.10', common_specs), + ('libXvMC', '1.0.9', common_specs), + ('libXxf86dga', '1.1.4', common_specs), + ('libXxf86vm', '1.1.4', common_specs), + ('libdmx', '1.1.3', common_specs), + ('libpciaccess', '0.13.4', common_specs), + ('libxkbfile', '1.0.9', common_specs), + ('libxshmfence', '1.2', common_specs), + ('xcb-util', '0.4.0', common_specs), + ('xcb-util-image', '0.4.0', common_specs), + ('xcb-util-keysyms', '0.4.0', common_specs), + ('xcb-util-renderutil', '0.3.9', common_specs), + ('xcb-util-wm', '0.4.1', common_specs), + ('xcb-util-cursor', '0.1.3', common_specs), +] + +# Python is required for xcb-proto +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +# 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': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib', + 'lib/python%s/site-packages/xcbgen' % pyshortver, 'lib/pkgconfig', 'share/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb index f735807177..556bda9f6e 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -23,6 +23,8 @@ builddependencies = [ dependencies = [ ('freetype', '2.6.5'), ('fontconfig', '2.12.1'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] default_easyblock = 'ConfigureMake' -- GitLab From 1cd35e36a2f2177505dba9c8e0f968c4a5cf8c3e Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 11 Oct 2016 11:49:17 +0200 Subject: [PATCH 612/701] * Renamed Pillow to make clear that this version depends on freetype 2.6.3. * Adjusted dependencies of scikit-image to matplotlib and Pillow for freetype 2.6.3. --- ...Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb} | 5 ++++- .../scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb | 6 ++++-- 2 files changed, 8 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/Pillow/{Pillow-3.2.0-foss-2016a-Python-2.7.11.eb => Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb} (85%) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb similarity index 85% rename from easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11.eb rename to easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb index b7a1d9ade1..16cea8d33b 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -13,13 +13,16 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +freetype_ver = '2.6.3' +versionsuffix += '-freetype-%s' % freetype_ver + dependencies = [ ('Python', '2.7.11'), ('libjpeg-turbo', '1.4.2','-NASM-2.12.01'), ('libpng', '1.6.21'), ('zlib', '1.2.8'), ('LibTIFF', '4.0.6'), - ('freetype', '2.6.3'), + ('freetype', freetype_ver), ] options = {'modulename': 'PIL'} diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb index fd95fa30d2..4f0de6e8da 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-foss-2016a-Python-2.7.11.eb @@ -15,12 +15,14 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +freetype_ver = '2.6.3' + dependencies = [ ('Python', '2.7.11'), ('Qhull', '2015.2'), - ('matplotlib', '1.5.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix + '-freetype-%s' % freetype_ver), ('networkx', '1.11', versionsuffix), - ('Pillow', '3.2.0', versionsuffix), + ('Pillow', '3.2.0', versionsuffix + '-freetype-%s' % freetype_ver), ] options = {'modulename': 'skimage'} -- GitLab From 87490e1b53faf57b95a8e6fb4deed920e1542859 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2016 12:48:08 +0200 Subject: [PATCH 613/701] stick to SUNDIALS 2.6.2, add 3to2 as build dep, enable running of Cantera tests --- .../3to2-1.1.1-intel-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ ...Cantera-2.2.1-intel-2016b-Python-2.7.12.eb | 15 +++++++---- 2 files changed, 35 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..264a6e4ac8 --- /dev/null +++ b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = '3to2' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/3to2' +description = """lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x + into Python version 2.x.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [('Python', '2.7.12')] + +options = {'modulename': 'lib3to2'} + +sanity_check_paths = { + 'files': ['bin/3to2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb index d95d3fc7c6..df2115bf2e 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb @@ -15,13 +15,18 @@ sources = ['v%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.12'), ('Boost', '1.61.0', versionsuffix), - ('SUNDIALS', '2.7.0'), + ('SUNDIALS', '2.6.2'), +] +builddependencies = [ + ('SCons', '2.5.0', versionsuffix), + ('3to2', '1.1.1', versionsuffix), ] -builddependencies = [('SCons', '2.5.0', versionsuffix)] -buildopts = 'CC="$CC" CXX="$CXX" env=all blas_lapack_libs=mkl_rt blas_lapack_dir=$BLAS_LAPACK_LIB_DIR' -buildopts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' -#runtest = 'test' +common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=mkl_rt blas_lapack_dir=$BLAS_LAPACK_LIB_DIR' +common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +buildopts = 'build ' + common_opts +runtest = 'test ' + common_opts +buildopts = 'install ' + common_opts prefix_arg = 'prefix=' modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -- GitLab From cf64ee0fb6e4820dcb6d8bdf86b742a81132dd89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2016 12:48:46 +0200 Subject: [PATCH 614/701] use 'letter_dir_for' function rather than just grabbing 1st letter of software name in easyconfigs tests --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3deb2e88ee..3de6473cca 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -46,7 +46,7 @@ from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.framework.easyblock import EasyBlock from easybuild.framework.easyconfig.default import DEFAULT_CONFIG from easybuild.framework.easyconfig.easyconfig import EasyConfig -from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, resolve_template +from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for, resolve_template from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config @@ -211,7 +211,7 @@ def template_easyconfig_test(self, spec): name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) # make sure easyconfig file is in expected location - expected_subdir = os.path.join('easybuild', 'easyconfigs', name.lower()[0], name) + expected_subdir = os.path.join('easybuild', 'easyconfigs', letter_dir_for(name), name) subdir = os.path.join(*spec.split(os.path.sep)[-5:-1]) fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) self.assertEqual(expected_subdir, subdir, fail_msg) -- GitLab From 2933a74b36b309d5b7bfd3507f2a59c28125f363 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2016 12:57:38 +0200 Subject: [PATCH 615/701] add easyconfig for SUNDIALS 2.6.2 --- .../s/SUNDIALS/SUNDIALS-2.6.2-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.6.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.6.2-intel-2016b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.6.2-intel-2016b.eb new file mode 100644 index 0000000000..db3419830f --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.6.2-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '2.6.2' + +homepage = 'http://computation.llnl.gov/projects/sundials' +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['http://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.6.2')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in solvers] + ['include/%s' % s for s in solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' -- GitLab From fb6e46bc6cbfbe8809d577b9c07d8416d99fefb5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2016 13:32:45 +0200 Subject: [PATCH 616/701] fix test_easyconfig_locations w.r.t. '0' letter dir used for 3to2 --- 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 3de6473cca..55faff811d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -169,7 +169,7 @@ class EasyConfigTest(TestCase): def test_easyconfig_locations(self): """Make sure all easyconfigs files are in the right location.""" - easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[a-z]/[^/]+$') + easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$') topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) for (dirpath, _, filenames) in os.walk(topdir): # ignore git/svn dirs -- GitLab From 1fbe2a84a6343e8580305e2a7d011d73e64f4f20 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 11 Oct 2016 14:10:49 +0200 Subject: [PATCH 617/701] Create a goolfc toolchain using CUDA 8.0.44 and the latest versions of the dependencies. CUDA 8.0.44 GCC 5.4.0-2.26 (Cuda still doesn't support any newer GCC compiler) FFTW 3.3.5 OpenBLAS 0.2.19/Lapack 3.6.1 OpenMPI 2.0.1 Scalapack 2.0.2 --- .../c/CUDA/CUDA-8.0.44-GCC-5.4.0-2.26.eb | 19 +++++++ .../f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb | 34 +++++++++++++ .../g/gcccuda/gcccuda-2016.10.0.eb | 21 ++++++++ .../easyconfigs/g/gompic/gompic-2016.10.0.eb | 23 +++++++++ .../easyconfigs/g/goolfc/goolfc-2016.10.0.eb | 38 ++++++++++++++ .../h/hwloc/hwloc-1.11.4-gcccuda-2016.10.0.eb | 23 +++++++++ ...AS-0.2.19-gompic-2016.10.0-LAPACK-3.6.1.eb | 49 +++++++++++++++++++ .../OpenMPI-2.0.1-gcccuda-2016.10.0.eb | 38 ++++++++++++++ ...-2016.10.0-OpenBLAS-0.2.19-LAPACK-3.6.1.eb | 25 ++++++++++ 9 files changed, 270 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb create mode 100644 easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.0.eb create mode 100644 easybuild/easyconfigs/g/gompic/gompic-2016.10.0.eb create mode 100644 easybuild/easyconfigs/g/goolfc/goolfc-2016.10.0.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.0.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10.0-LAPACK-3.6.1.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.10.0-OpenBLAS-0.2.19-LAPACK-3.6.1.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..414d7ab092 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-GCC-5.4.0-2.26.eb @@ -0,0 +1,19 @@ +name = 'CUDA' +version = '8.0.44' + +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': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = [ + 'http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/', + 'https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/prod/local_installers/' +] + +sources = ['%(namelower)s_%(version)s_linux-run'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb new file mode 100644 index 0000000000..c7b43ae2f7 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +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': 'gompic', 'version': '2016.10.0'} +toolchainopts = {'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-avx --enable-avx2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-avx --enable-avx2 --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/g/gcccuda/gcccuda-2016.10.0.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.0.eb new file mode 100644 index 0000000000..3d0ba0c9cf --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.0.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2016.10.0' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '5.4.0-2.26' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('CUDA', '8.0.44', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2016.10.0.eb b/easybuild/easyconfigs/g/gompic/gompic-2016.10.0.eb new file mode 100644 index 0000000000..b0c994f8de --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2016.10.0.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2016.10.0' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, + including OpenMPI for MPI support with CUDA features enabled.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '5.4.0-2.26' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, # part of gcccuda + ('CUDA', '8.0.44', '', comp), # part of gcccuda + ('OpenMPI', '2.0.1', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.0.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.0.eb new file mode 100644 index 0000000000..6fd9d7c78b --- /dev/null +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.0.eb @@ -0,0 +1,38 @@ +easyblock = "Toolchain" + +name = 'goolfc' +version = '2016.10.0' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '5.4.0-2.26' +comp = (comp_name, comp_ver) + +# toolchain used to build goolfc dependencies +comp_mpi_tc_name = 'gompic' +comp_mpi_tc_ver = version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.6.1' +blas = '-%s-%s%s' % (blaslib, blasver, blassuff) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, # part of gompic + ('CUDA', '8.0.44', '', comp), # part of gompic + ('OpenMPI', '2.0.1', '', ('gcccuda', version)), # part of gompic + (blaslib, blasver, blassuff, comp_mpi_tc), + ('FFTW', '3.3.5', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.0.eb new file mode 100644 index 0000000000..20cd96a781 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.4' + +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': 'gcccuda', 'version': '2016.10.0'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10.0-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10.0-LAPACK-3.6.1.eb new file mode 100644 index 0000000000..665e61e6ba --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10.0-LAPACK-3.6.1.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.19' + +lapackver = '3.6.1' +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': 'gompic', 'version': '2016.10.0'} + +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" + +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-2.0.1-gcccuda-2016.10.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.0.eb new file mode 100644 index 0000000000..6759d4aca3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.1' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'gcccuda', 'version': '2016.10.0'} + +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', +# 'OpenMPI-%(version)s-vt_cupti_events.patch', +#] + +dependencies = [('hwloc', '1.11.4')] + +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=$EBROOTHWLOC ' # hwloc support +configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "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] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.10.0-OpenBLAS-0.2.19-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.10.0-OpenBLAS-0.2.19-LAPACK-3.6.1.eb new file mode 100644 index 0000000000..dabe226ac2 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.10.0-OpenBLAS-0.2.19-LAPACK-3.6.1.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': 'gompic', 'version': '2016.10.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.6.1' + +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 5ccc895904db2b0e053d3108dec7855ab29ae77a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 11 Oct 2016 14:25:14 +0200 Subject: [PATCH 618/701] Add numactl-2.0.11-gcccuda-2016.10.0.eb config for the goo9lfc-2016.10.0 toolchain. --- .../numactl-2.0.11-gcccuda-2016.10.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-gcccuda-2016.10.0.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-gcccuda-2016.10.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-gcccuda-2016.10.0.eb new file mode 100644 index 0000000000..6ee99ec4e4 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-gcccuda-2016.10.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +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': 'gcccuda', 'version': '2016.10.0'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' -- GitLab From 02c0b0677fbe688b91aabc2e7444e581c92dd52e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 11 Oct 2016 15:04:12 +0200 Subject: [PATCH 619/701] {numlib}[{gompi,intel}/2016b] FFTW 3.3.5 (REVIEW) --- .../f/FFTW/FFTW-3.3.5-gompi-2016b.eb | 34 +++++++++++++++++++ .../f/FFTW/FFTW-3.3.5-intel-2016b.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016b.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016b.eb new file mode 100644 index 0000000000..e222c97b5d --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompi-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +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': '2016b'} +toolchainopts = {'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-3.3.5-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb new file mode 100644 index 0000000000..83943a28dd --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.5' + +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': '2016b'} +toolchainopts = {'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 84e49e7ea67a67099bdc5b8cd19cdad586a2347f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 11 Oct 2016 15:26:39 +0200 Subject: [PATCH 620/701] Remove quad prec from intel version --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb index 83943a28dd..6fcdd25eb5 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb @@ -15,19 +15,19 @@ 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-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']] + + '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']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], 'dirs': ['lib/pkgconfig'], } -- GitLab From 0d4521ddb7249cb3d67fb535c6176a60221cdc7d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 11 Oct 2016 16:04:49 +0200 Subject: [PATCH 621/701] {vis}[intel/2016b] FLTK/1.3.3 (REVIEW) --- .../f/FLTK/FLTK-1.3.3-intel-2016b.eb | 36 +++++++++++++++++++ .../x/xprop/xprop-1.2.2-intel-2016b.eb | 30 ++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb new file mode 100644 index 0000000000..0fe5be2665 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb @@ -0,0 +1,36 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.3' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('xprop', '1.2.2'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016b.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016b.eb new file mode 100644 index 0000000000..f011afc6c3 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.2' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +dependencies = [ + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 93fd4766a5299f02b27f4b0a019a203a82f843b7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 12 Oct 2016 14:00:00 +0800 Subject: [PATCH 622/701] remove redundant yambo patch --- .../QuantumESPRESSO-6.0-intel-2016b.eb | 2 +- .../QuantumESPRESSO-6.0_yambo-fixes.patch | 71 ------------------- 2 files changed, 1 insertion(+), 72 deletions(-) delete mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0_yambo-fixes.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb index a7b85783a2..cd4f2fd67f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb @@ -33,7 +33,7 @@ source_urls = [ ] patches = [ - 'QuantumESPRESSO-%(version)s_yambo-fixes.patch', + 'QuantumESPRESSO-5.4.0_yambo-fixes.patch', ] # source checksums diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0_yambo-fixes.patch deleted file mode 100644 index 8f94d88eb2..0000000000 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0_yambo-fixes.patch +++ /dev/null @@ -1,71 +0,0 @@ -* make sure -nofor_main is also used when $FC is defined as mpif90 for yambo -* fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output -* force ifort mangling in yambo's netcdf -author: Kenneth Hoste (HPC-UGent), adapted to qe-6.0 and yambo-3.4.2 by Miguel Dias Costa (National University of Singapore) ---- qe-6.0/yambo-3.4.2/configure.orig 2016-05-26 16:18:16.177156000 +0800 -+++ qe-6.0/yambo-3.4.2/configure 2016-05-26 16:20:31.929218336 +0800 -@@ -6238,7 +6238,7 @@ - ;; - *g95*) - ;; -- *ifort*) -+ *ifort*|*mpif90*) - $FC -v >& ver_ - VER_8=`grep 8. ver_ | wc -l` - VER_9=`grep 9. ver_ | wc -l` -@@ -6321,7 +6321,7 @@ - FCMFLAG="" - OMPFLAGS="-fopenmp" - ;; -- *ifort*) -+ *ifort*|*mpif90*) - CPU_FLAG="" - case "${FCVERSION}" in - *11* | *12* | *13* |*14* | *15* ) -@@ -6365,7 +6365,7 @@ - UFFLAGS="-g -O0 -fno-second-underscore" - FCMFLAG="" - ;; -- *ifort*) -+ *ifort*|*mpif90*) - CPU_FLAG="" - case "${FCVERSION}" in - *1*) -@@ -6413,7 +6413,7 @@ - UFFLAGS="-g -O0 -w" - OMPFLAGS="-openmp" - ;; -- *ifort*) -+ *ifort*|*mpif90*) - CPU_FLAG="" - case "${FCVERSION}" in - *1*) -@@ -6472,7 +6472,7 @@ - UFFLAGS="-g -O0 -w -tpp2" - OMPFLAGS="-openmp" - ;; -- *ifort*) -+ *ifort*|*mpif90*) - CPU_FLAG="" - case "${FCVERSION}" in - *11* | *12* | *13* |*14* |*15* ) -@@ -7651,7 +7651,7 @@ - - if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then - eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} -- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 >&5 -+ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 >&5 - if test -s conftest.er2 ; then - if ! test -n "`grep successful conftest.er2`" ; then - acx_F90_ok=no ; ---- qe-6.0/yambo-3.4.2/lib/netcdf/Makefile.loc.orig 2016-06-02 17:29:53.816844000 +0800 -+++ qe-6.0/yambo-3.4.2/lib/netcdf/Makefile.loc 2016-06-02 17:30:45.579476000 +0800 -@@ -40,7 +40,7 @@ - FC="$(f90)" \ - FCFLAGS="$(f77flags)" \ - FFLAGS="$(f77flags)" \ -- CPPFLAGS="$(netcdf_aux)" \ -+ CPPFLAGS="$(netcdf_aux) -DpgiFortran" \ - F90="$(f90)" \ - F77="$(f77)" \ - INSTALL_DIR="$(INSTALL_DIR)" ); \ -- GitLab From c14558c91951153fff1708381d4669e218d6a710 Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Wed, 12 Oct 2016 14:11:09 +0200 Subject: [PATCH 623/701] Add build targeting 64GiB and 128GiB machines --- easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb index 7984157482..f0b6a78950 100644 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb @@ -22,6 +22,10 @@ cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 - cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " # 1 billion array elements (1000 runs): requires ~22.4 GiB of memory cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " cmds_map = [('stream.c', cmds_str)] -- GitLab From 0811eb9919de070f8f50c48384ed48dd294b0791 Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Wed, 12 Oct 2016 14:19:26 +0200 Subject: [PATCH 624/701] Actually install the binaries --- easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb index f0b6a78950..9205395e4e 100644 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb @@ -29,10 +29,10 @@ cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=500000000 cmds_map = [('stream.c', cmds_str)] -files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B'], 'bin')] +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] sanity_check_paths = { - 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B'], + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], 'dirs': [], } -- GitLab From 3581cedbcabb987eb94dae96eb0bb9baf4252d1f Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Wed, 12 Oct 2016 14:37:12 +0200 Subject: [PATCH 625/701] STREAM 5.10 with 2016b toolchain --- .../s/STREAM/STREAM-5.10-intel-2016b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb new file mode 100644 index 0000000000..94341c99a0 --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb @@ -0,0 +1,41 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'http://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www.cs.virginia.edu/stream/FTP/Code/'] +sources = ['%(namelower)s.c'] +checksums = ['dd2941e3a28ff90a79b571273c10aacf'] + +skipsteps = ['source'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream.c', cmds_str)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' -- GitLab From 3dea1fdaf88545ed609f75003f63611c9e5c2b24 Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Wed, 12 Oct 2016 15:07:40 +0200 Subject: [PATCH 626/701] 5B elements does not build with the 2015a toolchain --- easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb index 9205395e4e..44cf8f84ff 100644 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb @@ -24,15 +24,13 @@ cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " # 2.5 billion array elements (1000 runs): requires ~56 GiB of memory cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " -# 5 billion array elements (1000 runs): requires ~111 GiB of memory -cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " cmds_map = [('stream.c', cmds_str)] -files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B'], 'bin')] sanity_check_paths = { - 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B'], 'dirs': [], } -- GitLab From cea6e793fbff4661ed3a376dbb21ed456d27b539 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 12 Oct 2016 15:40:57 +0200 Subject: [PATCH 627/701] more requested changes --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 9 ++++----- easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch | 11 ----------- 2 files changed, 4 insertions(+), 16 deletions(-) delete mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index f47f929afb..09fb675534 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -5,7 +5,8 @@ version = '4.1' homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' description = """ -The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes. +The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point +and global communication operations for a range of message sizes. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -15,9 +16,7 @@ source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] start_dir = 'src' prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' -buildopts = '-f make_mpich' - -patches = ['IMB-%(version)s_make_mpich.patch'] +buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" parallel = 1 @@ -28,4 +27,4 @@ sanity_check_paths = { 'dirs': ['bin','doc'] } -moduleclass = 'tools' +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch b/easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch deleted file mode 100644 index 6805a1bc3c..0000000000 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch +++ /dev/null @@ -1,11 +0,0 @@ -Prevent: Variable MPI_HOME="" does not seem to contain a valid mpicc. -Author: Fokke Dijkstra (University of Groningen) ---- src/make_mpich 2015-02-16 13:31:11.838082386 +0100 -+++ src/make_mpich 2015-02-16 13:40:19.000844455 +0100 -@@ -1,5 +1,5 @@ - # Enter root directory of mpich install --MPI_HOME= -+#MPI_HOME= - - MPICC=$(shell find ${MPI_HOME} -name mpicc -print) - -- GitLab From a8e361749fbb0e881b0fc27e64fff2b3a52a7520 Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Wed, 12 Oct 2016 15:48:03 +0200 Subject: [PATCH 628/701] Rust version 1.12 --- .../r/Rust/Rust-1.12.0-foss-2016b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb new file mode 100644 index 0000000000..ed6c626abd --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.12.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] + +builddependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' -- GitLab From 3fdc7a663ea16aa2e700d81831ee687fa3de0b41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Oct 2016 18:49:15 +0200 Subject: [PATCH 629/701] add easyconfig Biopython-1.68-intel-2016b-Python-2.7.12.eb --- ...iopython-1.68-intel-2016b-Python-2.7.12.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..953304846e --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.68' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From d31d4ec490bf28b8162fe4a511a4650d4c2cda74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Oct 2016 19:35:30 +0200 Subject: [PATCH 630/701] add easyconfig Ruby-2.3.1-intel-2016b.eb --- .../r/Ruby/Ruby-2.3.1-intel-2016b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.3.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1-intel-2016b.eb new file mode 100644 index 0000000000..f97bed944c --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1-intel-2016b.eb @@ -0,0 +1,63 @@ +# 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 = '2.3.1' + +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': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +ext_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.9.10', ext_options), + ('childprocess', '0.5.9', ext_options), + ('json', '1.8.3', ext_options), + ('cabin', '0.8.1', ext_options), + ('backports', '3.6.8', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '1.0.0', ext_options), + ('multipart-post', '2.0.0', ext_options), + ('faraday', '0.9.2', ext_options), + ('faraday_middleware', '0.10.0', ext_options), + ('highline', '1.7.8', ext_options), + ('net-http-pipeline', '1.0.1', ext_options), + ('net-http-persistent', '2.9.4', ext_options), + ('multi_json', '1.11.3', ext_options), + ('addressable', '2.4.0', ext_options), + ('gh', '0.14.0', ext_options), + ('launchy', '2.4.3', ext_options), + ('ethon', '0.8.1', ext_options), + ('typhoeus', '0.8.0', ext_options), + ('websocket', '1.2.3', ext_options), + ('pusher-client', '0.6.2', ext_options), + ('diff-lcs', '1.2.5', ext_options), + ('rspec-support', '3.4.1', ext_options), + ('rspec-mocks', '3.4.1', ext_options), + ('rspec-expectations', '3.4.0', ext_options), + ('rspec-core', '3.4.4', ext_options), + ('rspec', '3.4.0', ext_options), + ('rack', '1.6.4', ext_options), + ('rack-protection', '1.5.3', ext_options), + ('tilt', '2.0.2', ext_options), + ('sinatra', '1.4.7', ext_options), + ('rack-test', '0.6.3', ext_options), +] + +moduleclass = 'lang' -- GitLab From 8cd04d82b3d9bbc6f485c8470659d86521138e2a Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Wed, 12 Oct 2016 22:36:02 +0200 Subject: [PATCH 631/701] Update Python dependency version --- easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb index ed6c626abd..a97fb76cf4 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -builddependencies = [('Python', '2.7.11')] +builddependencies = [('Python', '2.7.12')] sanity_check_paths = { 'files': ['bin/rustc', 'bin/rustdoc'], -- GitLab From 15f9a654af9a0ce4258d18493edd86fa179638db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Oct 2016 09:30:28 +0200 Subject: [PATCH 632/701] add easyconfig dadi-1.7.0-intel-2016b-Python-2.7.12.eb --- .../dadi-1.7.0-intel-2016b-Python-2.7.12.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/d/dadi/dadi-1.7.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/d/dadi/dadi-1.7.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/dadi/dadi-1.7.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..dcb0dd7c09 --- /dev/null +++ b/easybuild/easyconfigs/d/dadi/dadi-1.7.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'dadi' +version = '1.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/gutenkunstlab/dadi' +description = """∂a∂i implements methods for demographic history and selection inference from genetic data, + based on diffusion approximations to the allele frequency spectrum.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://bitbucket.org/gutenkunstlab/dadi/get/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' -- GitLab From bfdc4f2c0343ebd8aba8f7e5953f0c5c428f7b29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Oct 2016 09:35:24 +0200 Subject: [PATCH 633/701] add patch to fix typo in GRIT 2.0.5 --- .../GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb | 1 + .../easyconfigs/g/GRIT/GRIT-2.0.5_fix-typo.patch | 15 +++++++++++++++ 2 files changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/g/GRIT/GRIT-2.0.5_fix-typo.patch diff --git a/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb index 2da2d712ac..ec4f6977d0 100644 --- a/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5-intel-2016b-Python-2.7.12.eb @@ -26,6 +26,7 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/nboley/grit/archive/'], 'source_tmpl': '%(version)s.tar.gz', + 'patches': ['GRIT-2.0.5_fix-typo.patch'], }), ] diff --git a/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5_fix-typo.patch b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5_fix-typo.patch new file mode 100644 index 0000000000..cb33a36d90 --- /dev/null +++ b/easybuild/easyconfigs/g/GRIT/GRIT-2.0.5_fix-typo.patch @@ -0,0 +1,15 @@ +fix typo resulting in AttributeError, see also https://github.com/nboley/grit/pull/3 +author: Kenneth Hoste (HPC-UGent) +diff --git a/grit/files/reads.py b/grit/files/reads.py +index 6228a43..a9cc2db 100644 +--- a/grit/files/reads.py ++++ b/grit/files/reads.py +@@ -957,7 +957,7 @@ class PolyAReads(Reads): + if reverse_read_strand in ('auto', None): + if ref_genes in([], None): + raise ValueError, "Determining reverse_read_strand requires reference genes" +- reverse_read_strand_params = Reads.determine_read_strand_param( ++ reverse_read_strand_params = determine_read_strand_params( + self, ref_genes, pairs_are_opp_strand, 'tes_exon', + 300, 50 ) + assert 'stranded' in reverse_read_strand_params -- GitLab From f417571519d0073674b8fb6d8e7428853f083875 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Oct 2016 12:55:55 +0200 Subject: [PATCH 634/701] fix icc/ifort/impi/imkl 2017.* versions, add intel/2017.00 definition --- ...26.eb => icc-2017.0.098-GCC-5.4.0-2.26.eb} | 2 +- ... => iccifort-2017.0.098-GCC-5.4.0-2.26.eb} | 2 +- ....eb => ifort-2017.0.098-GCC-5.4.0-2.26.eb} | 2 +- .../i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb | 4 ++-- ...017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb} | 2 +- ...098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb} | 4 ++-- .../easyconfigs/i/intel/intel-2017.00.eb | 24 +++++++++++++++++++ 7 files changed, 32 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/i/icc/{icc-2017.0.35-GCC-5.4.0-2.26.eb => icc-2017.0.098-GCC-5.4.0-2.26.eb} (97%) rename easybuild/easyconfigs/i/iccifort/{iccifort-2017.0.35-GCC-5.4.0-2.26.eb => iccifort-2017.0.098-GCC-5.4.0-2.26.eb} (95%) rename easybuild/easyconfigs/i/ifort/{ifort-2017.0.35-GCC-5.4.0-2.26.eb => ifort-2017.0.098-GCC-5.4.0-2.26.eb} (97%) rename easybuild/easyconfigs/i/imkl/{imkl-2017.0.98-iimpi-2017.00-GCC-5.4.0-2.26.eb => imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb} (98%) rename easybuild/easyconfigs/i/impi/{impi-2017.0.98-iccifort-2017.0.35-GCC-5.4.0-2.26.eb => impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb} (92%) create mode 100644 easybuild/easyconfigs/i/intel/intel-2017.00.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.35-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb similarity index 97% rename from easybuild/easyconfigs/i/icc/icc-2017.0.35-GCC-5.4.0-2.26.eb rename to easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb index 0c1088585e..d1cc307109 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.0.35-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,7 +1,7 @@ # This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild name = 'icc' -version = '2017.0.35' +version = '2017.0.098' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.35-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb similarity index 95% rename from easybuild/easyconfigs/i/iccifort/iccifort-2017.0.35-GCC-5.4.0-2.26.eb rename to easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 380fc915c1..3ed3f947b9 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.35-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -2,7 +2,7 @@ easyblock = "Toolchain" name = 'iccifort' -version = '2017.0.35' +version = '2017.0.098' versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.35-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb similarity index 97% rename from easybuild/easyconfigs/i/ifort/ifort-2017.0.35-GCC-5.4.0-2.26.eb rename to easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb index 3b5cada858..9f30cbac75 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.0.35-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,7 +1,7 @@ # This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild name = 'ifort' -version = '2017.0.35' +version = '2017.0.098' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb index b6b55ee8dc..1af95a3473 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -10,11 +10,11 @@ description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -compver = '2017.0.35' +compver = '2017.0.098' dependencies = [ ('icc', compver, versionsuffix), ('ifort', compver, versionsuffix), - ('impi', '2017.0.98', '', ('iccifort', '%s%s' % (compver, versionsuffix))), + ('impi', '2017.0.098', '', ('iccifort', '%s%s' % (compver, versionsuffix))), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.98-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb similarity index 98% rename from easybuild/easyconfigs/i/imkl/imkl-2017.0.98-iimpi-2017.00-GCC-5.4.0-2.26.eb rename to easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb index 39201957df..de287736f3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.0.98-iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -1,7 +1,7 @@ # This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild name = 'imkl' -version = '2017.0.98' +version = '2017.0.098' homepage = 'http://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, diff --git a/easybuild/easyconfigs/i/impi/impi-2017.0.98-iccifort-2017.0.35-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb similarity index 92% rename from easybuild/easyconfigs/i/impi/impi-2017.0.98-iccifort-2017.0.35-GCC-5.4.0-2.26.eb rename to easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 109a0bb59e..2f7a1cfdfd 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.0.98-iccifort-2017.0.35-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,14 +1,14 @@ # This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild name = 'impi' -version = '2017.0.98' +version = '2017.0.098' 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': '2017.0.35-GCC-5.4.0-2.26'} +toolchain = {'name': 'iccifort', 'version': '2017.0.098-GCC-5.4.0-2.26'} sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/intel/intel-2017.00.eb b/easybuild/easyconfigs/i/intel/intel-2017.00.eb new file mode 100644 index 0000000000..ad8be63148 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017.00.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2017.00' + +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 = '2017.0.098' +gccver = '5.4.0' +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '2017.0.098', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '2017.0.098', '', ('iimpi', version + gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From 90377612fc6c21e4880eeaab6ca0fd6bd798fa6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Oct 2016 12:57:19 +0200 Subject: [PATCH 635/701] add easyconfig for HPL 2.2 with intel/2017.00 --- .../easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb new file mode 100644 index 0000000000..48447ddb28 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +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': '2017.00'} +toolchainopts = {'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 adae534ef96a2b6cab4a1f694fd9f5ea62fec900 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Oct 2016 13:08:50 +0200 Subject: [PATCH 636/701] fix impi source spec --- .../impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 2f7a1cfdfd..867202a357 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -10,7 +10,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag toolchain = {'name': 'iccifort', 'version': '2017.0.098-GCC-5.4.0-2.26'} -sources = ['l_mpi_p_%(version)s.tgz'] +sources = ['l_mpi_%(version)s.tgz'] checksums = ['fc123875773816b7084a91e419d54d20'] -- GitLab From f5542817f8a4b2d215d735ae96309bbbcecfdc9d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 13 Oct 2016 13:38:56 +0200 Subject: [PATCH 637/701] Examples update for imkl/2017 --- .../i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb index de287736f3..341dbab7ed 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -22,11 +22,13 @@ interfaces = True postinstallcmds = [ # extract the examples - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', ] modextravars = { -- GitLab From c2dacc9333ce5eb9169cd73100f8ae2fc93e28fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Oct 2016 13:47:46 +0200 Subject: [PATCH 638/701] add easyconfig Biopython-1.68-intel-2016b-Python-3.5.2.eb --- ...Biopython-1.68-intel-2016b-Python-3.5.2.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..b22f51705c --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.68' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From 483a61dffd1abe479da14723461a506898be1b0e Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Thu, 13 Oct 2016 14:53:45 +0200 Subject: [PATCH 639/701] Add CMake dependency --- easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb index a97fb76cf4..de615e7620 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -builddependencies = [('Python', '2.7.12')] +builddependencies = [('Python', '2.7.12'), ('CMake','3.6.2')] sanity_check_paths = { 'files': ['bin/rustc', 'bin/rustdoc'], -- GitLab From c0095ca726e2747acc48e1bd4694d10af8d95cf9 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 13 Oct 2016 08:56:46 -0400 Subject: [PATCH 640/701] Add easyconfig for VTune 2017. --- easybuild/easyconfigs/v/VTune/VTune-2017.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2017.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017.eb b/easybuild/easyconfigs/v/VTune/VTune-2017.eb new file mode 100644 index 0000000000..13d248cd6c --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2017.eb @@ -0,0 +1,14 @@ +name = 'VTune' +version = '2017' + +homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From 07954d7c4a76ce7f2d0e7e9c169a05552c0b43fd Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Thu, 13 Oct 2016 14:59:28 +0100 Subject: [PATCH 641/701] Adding new toolchains for iomkl-2016.09-GCC-4.9.3-2.25 and iompi-2016.09-GCC-4.9.3-2.25 --- ...11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb | 48 +++++++++++++++++++ .../i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb | 20 ++++++++ .../i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb | 20 ++++++++ ...10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 41 ++++++++++++++++ 4 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..7fc4bb0100 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,48 @@ +name = 'imkl' +version = '11.3.3.210' + +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': 'iompi', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + + +# We want this in the module file. We send its output to /dev/null +# as otherwise it conflicts with the easybuild checking. +# It executes compilervars.sh which in turn executes several more scripts +# setting up the environment for icc etc. +modtclfooter = ''' +if [module-info mode load] { + set chan [open /dev/null a] + puts $chan "echo intel64" + puts $chan "source $root/bin/compilervars.sh" +} +''' + + +license_file = '/gpfs/apps/intel/LicenseManager/current/INTEL.lic' + +interfaces = True + +moduleclass = 'numlib' + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES' : '%(installdir)s/mkl/examples/', +} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..e9a72d1cbc --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '2016.09-GCC-4.9.3-2.25' + +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 = '2016.3.210-GCC-4.9.3-2.25' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('OpenMPI', '1.10.2', '', ('iccifort', compver)), + ('imkl', '11.3.3.210', '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..a5170410e3 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iompi' +version = '2016.09-GCC-4.9.3-2.25' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210-GCC-4.9.3-2.25' + +dependencies = [ + ('OpenMPI', '1.10.2', '', ('iccifort', compver)), + ('icc', compver), + ('ifort', compver), +] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..5de853b009 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} + +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=/usr/local/packages/hwloc ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-tm=/usr/local/packages/adaptive/torque ' # we want torque support as well + + +configopts += '--enable-debug ' + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'), ('libpciaccess-devel'), ('libudev-devel', 'systemd-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 libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +modextravars = { + "MXM_LOG_LEVEL": "ERROR", + "MXM_LOG_FILE": "/dev/stderr", +} + +moduleclass = 'mpi' -- GitLab From ac0f87225a974feb0d3092ff6ad768f54282f092 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Thu, 13 Oct 2016 15:09:31 +0100 Subject: [PATCH 642/701] Updating imkl to be like the others in upstream --- ...11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb | 22 +++++-------------- 1 file changed, 5 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb index 7fc4bb0100..bbbfc083fb 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-4.9.3-2.25.eb @@ -14,25 +14,11 @@ checksums = ['f72546df27f5ebb0941b5d21fd804e34'] dontcreateinstalldir = 'True' - -# We want this in the module file. We send its output to /dev/null -# as otherwise it conflicts with the easybuild checking. -# It executes compilervars.sh which in turn executes several more scripts -# setting up the environment for icc etc. -modtclfooter = ''' -if [module-info mode load] { - set chan [open /dev/null a] - puts $chan "echo intel64" - puts $chan "source $root/bin/compilervars.sh" -} -''' - - -license_file = '/gpfs/apps/intel/LicenseManager/current/INTEL.lic' +components = ['intel-mkl'] interfaces = True -moduleclass = 'numlib' +license_file = HOME + '/licenses/intel/license.lic' postinstallcmds = [ # extract the examples @@ -44,5 +30,7 @@ postinstallcmds = [ ] modextravars = { - 'MKL_EXAMPLES' : '%(installdir)s/mkl/examples/', + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', } + +moduleclass = 'numlib' -- GitLab From 30993ba3a23df3400223e079cdf4d1b7b61b8db5 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Thu, 13 Oct 2016 15:13:29 +0100 Subject: [PATCH 643/701] Updating OpenMPI to be like similar files on upstream --- ...10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 20 +++++++++---------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 5de853b009..2320c2ab64 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -9,23 +9,20 @@ description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -configopts += '--with-hwloc=/usr/local/packages/hwloc ' # hwloc support +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-tm=/usr/local/packages/adaptive/torque ' # we want torque support as well - -configopts += '--enable-debug ' +dependencies = [('hwloc', '1.11.3')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'), ('libpciaccess-devel'), ('libudev-devel', 'systemd-devel'),] +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 libs] + @@ -33,9 +30,10 @@ sanity_check_paths = { 'dirs': ["include/openmpi/ompi/mpi/cxx"], } -modextravars = { - "MXM_LOG_LEVEL": "ERROR", - "MXM_LOG_FILE": "/dev/stderr", -} +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] moduleclass = 'mpi' -- GitLab From 74405a7c10c5a6e0c03b3c1b774f6af3e535c7b0 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Thu, 13 Oct 2016 15:57:06 +0100 Subject: [PATCH 644/701] Adding missing dependencies for OpenMPI: hwloc and then numactl --- ...11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 25 +++++++++++++++++++ ...0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..701adb8479 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +# Automatically converted from hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +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': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} + +dependencies = [('numactl', '2.0.11')] + +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/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..734efafdaf --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +# Automatically converted from numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +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': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' \ No newline at end of file -- GitLab From 215efabdb5300d98116e159a077f99b8b7076d25 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 12:22:42 +0100 Subject: [PATCH 645/701] Responding to comments. Bumping OpenMPI to 1.10.4 and removing local comments. --- .../hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 -- easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- .../numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 4 +--- ...b => OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb} | 2 +- 4 files changed, 3 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb => OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb} (98%) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 701adb8479..d786ed3e2f 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,5 +1,3 @@ -# Automatically converted from hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb -# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py easyblock = 'ConfigureMake' name = 'hwloc' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb index e9a72d1cbc..cf9954cf88 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -13,7 +13,7 @@ compver = '2016.3.210-GCC-4.9.3-2.25' dependencies = [ ('icc', compver), ('ifort', compver), - ('OpenMPI', '1.10.2', '', ('iccifort', compver)), + ('OpenMPI', '1.10.4', '', ('iccifort', compver)), ('imkl', '11.3.3.210', '', ('iompi', version)), ] diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 734efafdaf..61b226e7c4 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,5 +1,3 @@ -# Automatically converted from numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb -# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py easyblock = 'ConfigureMake' name = 'numactl' @@ -22,4 +20,4 @@ sanity_check_paths = { 'dirs': ['share/man', 'include'] } -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb similarity index 98% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 2320c2ab64..c16d7bf245 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' -version = '1.10.2' +version = '1.10.4' homepage = 'http://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" -- GitLab From 74e6a79ff72b287bb0dd5f8a205b6b06bf93307d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Oct 2016 13:27:48 +0200 Subject: [PATCH 646/701] {devel}[foss/2016b] CMake 3.6.2 (REVIEW) --- .../c/CMake/CMake-3.6.2-foss-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb new file mode 100644 index 0000000000..adb0724437 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.2' + +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': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # 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', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From f1716237c8182b1bd8a5145dc9fd4d6d3e0a1c72 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 12:31:23 +0100 Subject: [PATCH 647/701] Bumping OpenMPI 10 1.10.4 in iompi-2016.09-GCC-4.9.3-2.25.eb --- easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb index a5170410e3..3c9854b3e1 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.3.210-GCC-4.9.3-2.25' dependencies = [ - ('OpenMPI', '1.10.2', '', ('iccifort', compver)), + ('OpenMPI', '1.10.4', '', ('iccifort', compver)), ('icc', compver), ('ifort', compver), ] -- GitLab From b14ee7220da1bbc74379dc8da03d2b4e8e57ca11 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Oct 2016 14:03:06 +0200 Subject: [PATCH 648/701] {vis}[foss/2016b] Mesa 12.0.2 (REVIEW) --- .../l/libdrm/libdrm-2.4.70-foss-2016b.eb | 24 ++++++++ .../libxml2-2.9.4-foss-2016b-Python-2.7.12.eb | 24 ++++++++ .../Mako-1.0.4-foss-2016b-Python-2.7.12.eb | 22 +++++++ .../m/Mesa/Mesa-12.0.2-foss-2016b.eb | 59 +++++++++++++++++++ .../n/nettle/nettle-3.2-foss-2016b.eb | 28 +++++++++ 5 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb new file mode 100644 index 0000000000..5d9e8ac938 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.70' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016b'} + +dependencies = [ + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a047fc32c8 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +name = 'libxml2' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +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': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), + ('Python', '2.7.12'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..eaaa1eb1ea --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb new file mode 100644 index 0000000000..8152b5bb38 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb @@ -0,0 +1,59 @@ +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '12.0.2' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('Mako', '1.0.4', '-Python-2.7.12'), + ('libxml2', '2.9.4', '-Python-2.7.12'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('nettle', '3.2'), + ('libdrm', '2.4.70'), + ('LLVM', '3.8.1'), + ('X11', '20160819'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, + 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb new file mode 100644 index 0000000000..d8b0e1009d --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.2' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' -- GitLab From da243ab23699203f7a4d89f21cadcce296c9cd37 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Oct 2016 14:51:46 +0200 Subject: [PATCH 649/701] {vis}[foss/2016b] FLTK 1.3.3 (REVIEW) --- .../f/FLTK/FLTK-1.3.3-foss-2016b.eb | 36 +++++++++++++++++++ .../l/libGLU/libGLU-9.0.0-foss-2016b.eb | 24 +++++++++++++ .../x/xprop/xprop-1.2.2-foss-2016b.eb | 30 ++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb new file mode 100644 index 0000000000..7c571b0ec9 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb @@ -0,0 +1,36 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.3' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('xprop', '1.2.2'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016b.eb new file mode 100644 index 0000000000..361489070d --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '12.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016b.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016b.eb new file mode 100644 index 0000000000..abb82d5158 --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.2' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +dependencies = [ + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From f931f66fca8b06c64a9a8b1fe7a23914bc34ff1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2016 16:20:30 +0200 Subject: [PATCH 650/701] add easyconfig HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb --- .../HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..22cd32989a --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'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 95b29a4626a0b264462bd78571318d1a4d86447a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2016 10:20:57 +0200 Subject: [PATCH 651/701] add easyconfig requests-2.11.1-intel-2016b-Python-3.5.2.eb, add easyconfig requests-2.11.1-intel-2016b-Python-2.7.12.eb --- ...quests-2.11.1-intel-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ ...equests-2.11.1-intel-2016b-Python-3.5.2.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..28824ad2fc --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..19001f1fa6 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.11.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' -- GitLab From bed9d654f559b6b7e5e6d43ccf990fcab31e59de Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 17 Oct 2016 15:00:12 +0200 Subject: [PATCH 652/701] add easyconfig LASTZ-1.02.00-goolf-1.7.20.eb --- .../l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb new file mode 100644 index 0000000000..d7a88ce495 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'LASTZ' +version = '1.02.00' + +homepage = 'http://www.bx.psu.edu/~rsharris/lastz/' + +description = """LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to + handle sequences the size of human chromosomes and from different species, it is also useful for sequences + produced by NGS sequencing technologies such as Roche 454.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +# the tarball includes some test data which is not copied when doing the "make install" step. +# We use the buildininstalldir option to keep this test data in the %(installdir)s +buildininstalldir = True + +parallel = 1 + +unpack_options = '--strip-components=1' + +skipsteps = ['configure'] + +# by default definedForAll variable in src/Makefile contains -Werror which works with gcc-4.4 +# but crashes with newer gcc versions so we override definedForAll to remove the -Werror option +buildopts = " definedForAll='-Wall -Wextra -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE'" + +# use the LASTZ_INSTALL variable to define the directory where to copy the binaries during "make install" step +# Tarball includes an empty bin/ folder. In case the tarball doesn't include a bin/ folder you can do +# preinstallopts = 'mkdir %(installdir)s/bin/ && ' +installopts = " LASTZ_INSTALL='%(installdir)s/bin'" + +sanity_check_paths = { + 'files': ["bin/lastz", "bin/lastz_D"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 49db5643421c38406903ef43d1685920fd1d0c59 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 17 Oct 2016 14:36:12 +0100 Subject: [PATCH 653/701] add easyconfig pandas-0.19.0-foss-2016b-Python-2.7.12.eb, add easyconfig pandas-0.19.0-foss-2016b-Python-3.5.2.eb, add easyconfig pandas-0.19.0-intel-2016b-Python-2.7.12.eb, add easyconfig pandas-0.19.0-intel-2016b-Python-3.5.2.eb --- .../pandas-0.19.0-foss-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ .../pandas-0.19.0-foss-2016b-Python-3.5.2.eb | 23 +++++++++++++++++++ ...pandas-0.19.0-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ .../pandas-0.19.0-intel-2016b-Python-3.5.2.eb | 23 +++++++++++++++++++ 4 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..d10a536e67 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.0' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..66017ec403 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.0' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..8829139b1b --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.0' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..823a55912c --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.0' +versionsuffix = '-Python-%(pyver)s' + +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 8693e0b9b3df082e712687975284284e6eac42b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2016 10:34:33 +0200 Subject: [PATCH 654/701] add easyconfig StringTie-1.3.0-intel-2016b.eb --- .../StringTie/StringTie-1.3.0-intel-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb new file mode 100644 index 0000000000..424d2b7aeb --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '1.3.0' + +homepage = 'http://ccb.jhu.edu/software/stringtie/' +description = """StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCELOWER_TAR_GZ] + +files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/stringtie'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c891c80e22be44b961a9c34c7d833e20586952d7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 19 Oct 2016 13:18:21 +0200 Subject: [PATCH 655/701] {vis}[intel/2016b] wxPython 3.0.2.0 (REVIEW) --- .../a/ATK/ATK-2.22.0-intel-2016b.eb | 34 ++++++++++++++++ .../d/DBus/DBus-1.10.12-intel-2016b.eb | 24 +++++++++++ .../dbus-glib/dbus-glib-0.108-intel-2016b.eb | 25 ++++++++++++ .../g/GConf/GConf-3.2.6-intel-2016b.eb | 39 ++++++++++++++++++ .../GST-plugins-base-0.10.36-intel-2016b.eb | 35 ++++++++++++++++ .../GStreamer-0.10.36-intel-2016b.eb | 40 +++++++++++++++++++ .../g/GTK+/GTK+-2.24.31-intel-2016b.eb | 25 ++++++++++++ .../Gdk-Pixbuf-2.36.0-intel-2016b.eb | 34 ++++++++++++++++ ...intltool-0.51.0-intel-2016b-Perl-5.24.0.eb | 25 ++++++++++++ ...ython-3.0.2.0-intel-2016b-Python-2.7.12.eb | 34 ++++++++++++++++ ...-Parser-2.44_01-intel-2016b-Perl-5.24.0.eb | 27 +++++++++++++ 11 files changed, 342 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.108-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016b-Perl-5.24.0.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb new file mode 100644 index 0000000000..9b536efda0 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.22.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +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': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('GObject-Introspection', '1.49.1') +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb new file mode 100644 index 0000000000..7071afdb2c --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.10.12' + +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': '2016b'} + +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', SHLIB_EXT]], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.108-intel-2016b.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.108-intel-2016b.eb new file mode 100644 index 0000000000..318a8a890a --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.108-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.108' + +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': '2016b'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('DBus', '1.10.12'), + ('expat', '2.2.0'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb new file mode 100644 index 0000000000..a184de7e11 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2016b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +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': '2016b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('dbus-glib', '0.108'), + ('GLib', '2.49.5'), + ('GObject-Introspection', '1.49.1'), + ('libxml2', '2.9.4'), + ('GTK+', '2.24.31'), + ('intltool', '0.51.0', '-Perl-5.24.0'), +] + +configopts = '--disable-orbit ' + +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/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb new file mode 100644 index 0000000000..743a59e91a --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +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': '2016b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [('GStreamer', '0.10.36')] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) 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-2016b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb new file mode 100644 index 0000000000..a0214562e2 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +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': '2016b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('GObject-Introspection', '1.49.1'), + ('zlib', '1.2.8'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) 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+-2.24.31-intel-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb new file mode 100644 index 0000000000..78f4ad00b7 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.31' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.22.0'), + ('Gdk-Pixbuf', '2.36.0'), + ('Pango', '1.40.3'), + ('GObject-Introspection', '1.49.1'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb new file mode 100644 index 0000000000..4d84597d62 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-intel-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.36.0' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.49.1') +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..c5a095b3f6 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' +versionsuffix = '-Perl-5.24.0' + +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': '2016b'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('XML-Parser', '2.44_01', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..73dad53861 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,34 @@ +name = 'wxPython' +version = '3.0.2.0' +versionsuffix = "-Python-%(pyver)s" + +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': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] + +patches = ['%(name)s_%(version)s_intel.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('libpng', '1.6.24'), + ('zlib', '1.2.8'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), + ('expat', '2.2.0'), + ('GTK+', '2.24.31'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..d7ce4573e1 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.44_01' +versionsuffix = '-Perl-%(perlver)s' + +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': 'intel', 'version': '2016b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.24.0'), + ('expat', '2.2.0') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], +} + +moduleclass = 'data' -- GitLab From 8cf50540954adabad0801bbdecc1c668b20b911a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2016 19:22:57 +0200 Subject: [PATCH 656/701] add easyconfig mypy-0.4.5-intel-2016b.eb --- .../m/mypy/mypy-0.4.5-intel-2016b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb diff --git a/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb b/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb new file mode 100644 index 0000000000..9a4921fa74 --- /dev/null +++ b/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'mypy' +version = '0.4.5' + +homepage = 'http://www.mypy-lang.org/' +description = """Optional static typing for Python""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '3.5.2')] + +exts_list = [ + ('typed-ast', '0.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typed-ast'], + 'modulename': 'typed_ast', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/mypy-lang'], + 'source_tmpl': 'mypy-lang-%(version)s.tar.gz', + 'modulename': 'mypy_lang', + }), +] + +# 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/mypy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' -- GitLab From 4ec368166459ea701600a38d79f1581de3ed2a21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2016 19:28:08 +0200 Subject: [PATCH 657/701] fix sanity check by making sure $PYTHONPATH is set correctly --- easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb b/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb index 9a4921fa74..7ebbaca141 100644 --- a/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb +++ b/easybuild/easyconfigs/m/mypy/mypy-0.4.5-intel-2016b.eb @@ -21,13 +21,14 @@ exts_list = [ (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/mypy-lang'], 'source_tmpl': 'mypy-lang-%(version)s.tar.gz', - 'modulename': 'mypy_lang', }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + sanity_check_paths = { 'files': ['bin/mypy'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], -- GitLab From 330a4be23ab09cce718462084df9abbfc089540a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Oct 2016 14:58:47 +0200 Subject: [PATCH 658/701] add easyconfig hanythingondemand-3.2.0-cli.eb, add easyconfig hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb --- .../hanythingondemand-3.2.0-cli.eb | 42 +++++++++++++++++++ ...ndemand-3.2.0-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb new file mode 100644 index 0000000000..7e255dbc21 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.0' +versionsuffix = '-cli' + +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': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) +dependencies = [ + ('pbs_python', '4.6.0'), + ('vsc-base', '2.5.1'), +] + +use_easy_install = True +zipped_egg = True + +# use 'hod' rather than 'hanythingondemand' in module name +modaltsoftname = 'hod' + +options = {'modulename': 'hod'} + +modextravars = { + # site-specific settings, hence commented out + # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) + #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # specify location on shared 'scratch' filesystem for HOD working directories + #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ea99d52247 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.0' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime +dependencies = [ + ('Python', '2.7.12'), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.3', versionsuffix), +] + +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'hod'} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' -- GitLab From 8335ca81fdd984b961935d564c5cf2ee8de62e49 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 24 Oct 2016 10:21:15 +0200 Subject: [PATCH 659/701] The patches block in OpenMPI for cuda is no longer needed. This is true from OpeMPI versions 1.10 and upwards. --- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.0.eb index 6759d4aca3..c4792dca19 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.0.eb @@ -12,11 +12,6 @@ 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', -# 'OpenMPI-%(version)s-vt_cupti_events.patch', -#] - dependencies = [('hwloc', '1.11.4')] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' -- GitLab From 3a05c4bd6072fe4f97d257f5f1b255c09176b446 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 24 Oct 2016 10:29:24 +0200 Subject: [PATCH 660/701] For the time being, drop --enable-avx2 from the configopts of FFTW. Need to have a way to detect available features of the cpu used for building and add flags accordingly. --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb index c7b43ae2f7..6df05f5634 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb @@ -16,10 +16,10 @@ source_urls = [homepage] common_configopts = "--enable-threads --enable-openmp --with-pic" configopts = [ - common_configopts + " --enable-single --enable-sse2 --enable-avx --enable-avx2 --enable-mpi", + common_configopts + " --enable-single --enable-sse2 --enable-avx --enable-mpi", common_configopts + " --enable-long-double --enable-mpi", common_configopts + " --enable-quad-precision", - common_configopts + " --enable-sse2 --enable-avx --enable-avx2 --enable-mpi", # default as last + common_configopts + " --enable-sse2 --enable-avx --enable-mpi", # default as last ] sanity_check_paths = { -- GitLab From 0f98864cd461e2d8e5df95458ac2db8f9f18c227 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2016 12:56:15 +0200 Subject: [PATCH 661/701] use $CC,$CXX rather than $I_MPI_CC,$I_MPI_CXX in patch for OpenFOAM 4.0 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch index 1afeb16c3a..6ad12341f4 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-cleanup.patch @@ -235,8 +235,8 @@ diff -ur OpenFOAM-4.0.orig/etc/config.sh/settings OpenFOAM-4.0/etc/config.sh/set - export WM_CFLAGS='-m64 -fPIC' - export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' - export WM_LDFLAGS='-m64' -+ export WM_CC=$I_MPI_CC -+ export WM_CXX=$I_MPI_CXX ++ export WM_CC=$CC ++ export WM_CXX=$CXX + export WM_CFLAGS=$CFLAGS + export WM_CXXFLAGS=$CXXFLAGS + export WM_LDFLAGS=$LDFLAGS -- GitLab From 752ba0b494c9e512d6a208bf064f3f07350a6d7d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 14:52:30 +0200 Subject: [PATCH 662/701] FLTK 1.3.3 patch for Octave (and maybe others) --- .../f/FLTK/FLTK-1.3.3-foss-2016a.eb | 2 + .../f/FLTK/FLTK-1.3.3-foss-2016b.eb | 2 + .../f/FLTK/FLTK-1.3.3-intel-2016a.eb | 2 + .../f/FLTK/FLTK-1.3.3-intel-2016b.eb | 2 + .../FLTK/FLTK-1.3.3_undefined_reference.patch | 46 +++++++++++++++++++ 5 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.3_undefined_reference.patch diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb index 0056b11391..228b99e49e 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016a.eb @@ -17,6 +17,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +patches = ['%(name)s-%(version)s_undefined_reference.patch'] + configopts = '--enable-shared --enable-threads --enable-xft' dependencies = [ diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb index 7c571b0ec9..4c82344219 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-foss-2016b.eb @@ -17,6 +17,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +patches = ['%(name)s-%(version)s_undefined_reference.patch'] + configopts = '--enable-shared --enable-threads --enable-xft' dependencies = [ diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb index d88b64d96a..efbb3a2282 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016a.eb @@ -17,6 +17,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +patches = ['%(name)s-%(version)s_undefined_reference.patch'] + configopts = '--enable-shared --enable-threads --enable-xft' dependencies = [ diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb index 0fe5be2665..7a909b4015 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3-intel-2016b.eb @@ -17,6 +17,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(namelower)s-%(version)s-source.tar.gz'] source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +patches = ['%(name)s-%(version)s_undefined_reference.patch'] + configopts = '--enable-shared --enable-threads --enable-xft' dependencies = [ diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3_undefined_reference.patch b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3_undefined_reference.patch new file mode 100644 index 0000000000..5ddc1900ed --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.3_undefined_reference.patch @@ -0,0 +1,46 @@ +#see https://groups.google.com/forum/#!topic/fltkgeneral/GT6i2KGCb3A +#and http://www.fltk.org/str.php?L3156 +# GNU Octave compains: +# error: octave-4.0.3/libinterp/dldfcn/PKG_ADD: octave-4.0.3/libinterp/dldfcn/__init_fltk__.oct: failed to load: FLTK/1.3.3-intel-2016b/lib/libfltk_gl.so.1.3: undefined symbol: _ZN18Fl_XFont_On_Demand5valueEv +Index: src/fl_font.cxx +=================================================================== +--- fltk-1.3.3/src/fl_font.cxx (revision 10503) ++++ fltk-1.3.3/src/fl_font.cxx (revision 10504) +@@ -55,6 +55,12 @@ + # include "fl_font_x.cxx" + #endif // WIN32 + ++#if ! (defined(WIN32) || defined(__APPLE__)) ++XFontStruct *fl_X_core_font() ++{ ++ return fl_xfont.value(); ++} ++#endif + + double fl_width(const char* c) { + if (c) return fl_width(c, (int) strlen(c)); +Index: src/gl_draw.cxx +=================================================================== +--- fltk-1.3.3/src/gl_draw.cxx (revision 10503) ++++ fltk-1.3.3/src/gl_draw.cxx (revision 10504) +@@ -81,7 +81,7 @@ + * then sorting through them at draw time (for normal X rendering) to find which one can + * render the current glyph... But for now, just use the first font in the list for GL... + */ +- XFontStruct *font = fl_xfont; ++ XFontStruct *font = fl_X_core_font(); + int base = font->min_char_or_byte2; + int count = font->max_char_or_byte2-base+1; + fl_fontsize->listbase = glGenLists(256); +Index: FL/x.H +=================================================================== +--- fltk-1.3.3/FL/x.H (revision 10503) ++++ fltk-1.3.3/FL/x.H (revision 10504) +@@ -132,6 +132,7 @@ + XFontStruct *ptr; + }; + extern FL_EXPORT Fl_XFont_On_Demand fl_xfont; ++extern FL_EXPORT XFontStruct* fl_X_core_font(); + + // this object contains all X-specific stuff about a window: + // Warning: this object is highly subject to change! -- GitLab From 3a57d1e3cfe25078ef59624cdb11842d29b3bd9c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:04:39 +0200 Subject: [PATCH 663/701] {lang}[dummy] Java 1.8.0_112 (REVIEW) --- easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb new file mode 100644 index 0000000000..6b87f36815 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_112' + +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 0983b48f3d1bff8a4b6d68f7bc21905f57729de3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:08:30 +0200 Subject: [PATCH 664/701] {vis}[intel/2016b] GraphicsMagick 1.3.25 (REVIEW) --- .../GraphicsMagick-1.3.25-intel-2016b.eb | 39 +++++++++++++++++++ .../GraphicsMagick-1.3.25_intel.patch | 13 +++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25_intel.patch diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2016b.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2016b.eb new file mode 100644 index 0000000000..20888d4d87 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2016b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.25' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] + +patches = ['%(name)s-%(version)s_intel.patch'] + +builddependencies = [ + ('libtool', '2.4.6'), +] + +dependencies = [ + ('X11', '20160819'), + ('bzip2', '1.0.6'), + ('freetype', '2.6.5'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), + ('libxml2', '2.9.4'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('Ghostscript', '9.19'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25_intel.patch b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25_intel.patch new file mode 100644 index 0000000000..1b8082e74b --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25_intel.patch @@ -0,0 +1,13 @@ +#Intel compiler does not understand __has_attribute(attribute +# Oct 24th 2016 by B. Hajgato (Free University Brussels - VUB) +--- GraphicsMagick-1.3.25/magick/common.h.orig 2016-09-05 21:20:24.000000000 +0200 ++++ GraphicsMagick-1.3.25/magick/common.h 2016-10-24 15:03:21.858939448 +0200 +@@ -128,7 +128,7 @@ + # define MAGICK_ATTRIBUTE(x) /*nothing*/ + # else + # define MAGICK_ATTRIBUTE(x) __attribute__(x) +-# if (defined(__clang__) || (defined(__GNUC__) && __GNUC__ >= 5)) ++# if (defined(__clang__) || ((defined(__GNUC__) && __GNUC__ >= 5) && !__INTEL_COMPILER)) + # define MAGICK_HAS_ATTRIBUTE(attribute) __has_attribute(attribute) + # else + # define MAGICK_HAS_ATTRIBUTE(attribute) (0) -- GitLab From 654c105aaadc8be8027bf2538465b5a7410ed363 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:11:00 +0200 Subject: [PATCH 665/701] {numlib}[intel/2016b] arpack-ng 3.4.0 (REVIEW) --- .../arpack-ng/arpack-ng-3.4.0-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2016b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2016b.eb new file mode 100644 index 0000000000..feba2c7b4c --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.4.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 617518b340c5069db15e7f676b2ae127541b8e73 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:13:28 +0200 Subject: [PATCH 666/701] {tools}[intel/2016b] GLPK 4.60 (REVIEW) --- .../g/GLPK/GLPK-4.60-intel-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb new file mode 100644 index 0000000000..66b0f5b8f2 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.60' + +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': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.1.1')] + +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' -- GitLab From 78a08ebde6c6dead3fe1c7da2fbe4c0412da5930 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:15:24 +0200 Subject: [PATCH 667/701] {numlib}[intel/2016b] SuiteSparse 4.5.3 w/ METIS 5.1.0 (REVIEW) --- ...iteSparse-4.5.3-intel-2016b-METIS-5.1.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016b-METIS-5.1.0.eb new file mode 100644 index 0000000000..5235dd9545 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016b-METIS-5.1.0.eb @@ -0,0 +1,20 @@ +name = 'SuiteSparse' +version = '4.5.3' + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From fc6e26373f9d72aa1f3a6e9a48e6678926d969e7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:17:18 +0200 Subject: [PATCH 668/701] {data}[intel/2016b] HDF5 1.8.17 serial (REVIEW) --- .../h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb new file mode 100644 index 0000000000..ded2abcfa1 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.17' +versionsuffix = '-serial' + +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': '2016b'} +toolchainopts = {'pic': True, 'usempi': False} + +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 fbd5b5aa1b1a340dcf128b54d579c5bfb6fa2bd4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:18:53 +0200 Subject: [PATCH 669/701] {vis}[intel/2016b] gnuplot 5.0.5 (REVIEW) --- .../g/gnuplot/gnuplot-5.0.5-intel-2016b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-2016b.eb new file mode 100644 index 0000000000..1181859b40 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-2016b.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/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 = '5.0.5' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.6'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('libgd', '2.2.3'), + ('Pango', '1.40.3'), + ('libcerf', '1.5'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From cc6c6a09c577d0c0eb85027e2030f6c074ec24d6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:20:26 +0200 Subject: [PATCH 670/701] {devel}[intel/2016b] gperf 3.0.4 (REVIEW) --- .../g/gperf/gperf-3.0.4-intel-2016b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016b.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016b.eb new file mode 100644 index 0000000000..4ada07243f --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2016b.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': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 2b9d0a6d127747e47e86f82a72a0556db6c53541 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:21:53 +0200 Subject: [PATCH 671/701] {math}[intel/2016b] libcerf 1.5 (REVIEW) --- .../l/libcerf/libcerf-1.5-intel-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2016b.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2016b.eb new file mode 100644 index 0000000000..0cce9f8c98 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.5' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """libcerf is a self-contained numeric library that provides an efficient and accurate + implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TGZ] +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 2b765033a3f39c6c5ffe526f02fe86a9d8a468af Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:24:16 +0200 Subject: [PATCH 672/701] {lib}[intel/2016b] libgd 2.2.3 (REVIEW) --- .../l/libgd/libgd-2.2.3-intel-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.2.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.3-intel-2016b.eb new file mode 100644 index 0000000000..3a99421ffa --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.3-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.2.3' + +homepage = 'http://libgd.bitbucket.org/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fontconfig', '2.12.1'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' -- GitLab From b13f9770952581934f4ea1c2b514a24600554acf Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:27:34 +0200 Subject: [PATCH 673/701] {numlib}[intel/2016b] qrupdate 1.1.2 (REVIEW) --- .../q/qrupdate/qrupdate-1.1.2-intel-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016b.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016b.eb new file mode 100644 index 0000000000..4c96735e49 --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['%(name)s-%(version)s_makeconf.patch'] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 007e3efccda1f85195c00a3d70a5edba2ed5d288 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Oct 2016 15:55:15 +0200 Subject: [PATCH 674/701] add easyconfig scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb, add easyconfig Qhull-2015.2-intel-2016b.eb, add easyconfig matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb, add easyconfig libpng-1.6.26-intel-2016b.eb, add easyconfig freetype-2.7-intel-2016b.eb --- .../f/freetype/freetype-2.7-intel-2016b.eb | 26 ++++++++++ .../l/libpng/libpng-1.6.26-intel-2016b.eb | 26 ++++++++++ ...plotlib-1.5.3-intel-2016b-Python-2.7.12.eb | 44 +++++++++++++++++ .../q/Qhull/Qhull-2015.2-intel-2016b.eb | 36 ++++++++++++++ ...-image-0.12.3-intel-2016b-Python-2.7.12.eb | 48 +++++++++++++++++++ 5 files changed, 180 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.26-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016b.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb new file mode 100644 index 0000000000..52d8477931 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb @@ -0,0 +1,26 @@ +name = 'freetype' +version = '2.7' + +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': '2016b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libpng', '1.6.26'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.26-intel-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.26-intel-2016b.eb new file mode 100644 index 0000000000..ba71624bd1 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.26-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.26' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2cd2414697 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.3' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('freetype', '2.7'), + ('libpng', '1.6.26'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# 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': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016b.eb new file mode 100644 index 0000000000..e282e73b71 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2016b.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2015.2' + +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': '2016b'} + +sources = ['%(namelower)s-%(version_major)s-src-7.%(version_minor)s.0.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = [ + 'Qhull-%(version)s-intel-fix.patch', + 'Qhull_pkgconfig.patch', +] + +builddependencies = [('CMake', '3.6.2')] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.%s' % SHLIB_EXT, 'lib/pkgconfig/qhull.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..87114134c7 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'scikit-image' +version = '0.12.3' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('Qhull', '2015.2'), + ('matplotlib', '1.5.3', versionsuffix), +] + +exts_list = [ + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + }), + ('Pillow', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pillow'], + 'modulename': 'PIL', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], + 'modulename': 'skimage', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +# 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': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' -- GitLab From a21d3751f5f6ecd9e49cd34b258f9f314387534e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Oct 2016 16:09:15 +0200 Subject: [PATCH 675/701] add easyconfig scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb, add easyconfig matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb --- ...tplotlib-1.5.3-intel-2016b-Python-3.5.2.eb | 44 +++++++++++++++++ ...t-image-0.12.3-intel-2016b-Python-3.5.2.eb | 48 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..1db14993c4 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.3' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('freetype', '2.7'), + ('libpng', '1.6.26'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# 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': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..bb4cf1ccf1 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'scikit-image' +version = '0.12.3' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('Qhull', '2015.2'), + ('matplotlib', '1.5.3', versionsuffix), +] + +exts_list = [ + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + }), + ('Pillow', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pillow'], + 'modulename': 'PIL', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], + 'modulename': 'skimage', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +# 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': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' -- GitLab From 1c96cb002f8e3d78cdb750d864817a3fc9d52313 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 10:40:34 +0200 Subject: [PATCH 676/701] add easyconfig RSEM-1.2.30-intel-2016b.eb --- .../r/RSEM/RSEM-1.2.30-intel-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb new file mode 100644 index 0000000000..5420a22996 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.2.30' + +homepage = 'http://deweylab.github.io/RSEM/' +description = """RNA-Seq by Expectation-Maximization""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['RSEM-%(version)s_makefiles.patch'] + +skipsteps = ['configure'] +installopts = "prefix=%(installdir)s" + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', 'bin/rsem-bam2wig', + 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'dirs': ['bin/samtools-1.3'], +} + +moduleclass = 'bio' -- GitLab From 4d91ffbae104cdd12e804bb0d06e936f8b5b0b17 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 10:47:28 +0200 Subject: [PATCH 677/701] include Pillow as a proper dep for scikit-image rather than as extension, since it has deps itself --- .../libjpeg-turbo-1.5.1-intel-2016b.eb | 30 +++++++++++++++++++ .../Pillow-3.4.2-intel-2016b-Python-2.7.12.eb | 27 +++++++++++++++++ .../Pillow-3.4.2-intel-2016b-Python-3.5.2.eb | 27 +++++++++++++++++ ...-image-0.12.3-intel-2016b-Python-2.7.12.eb | 5 +--- ...t-image-0.12.3-intel-2016b-Python-3.5.2.eb | 5 +--- 5 files changed, 86 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2016b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2016b.eb new file mode 100644 index 0000000000..ecf772ccf1 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.1' + +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': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.12.02'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..4667d2c7a6 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.4.2' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.26'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', '2.7'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..a95d247bb5 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.4.2-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '3.4.2' +versionsuffix = '-Python-%(pyver)s' + +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': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.26'), + ('zlib', '1.2.8'), + ('LibTIFF', '4.0.6'), + ('freetype', '2.7'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb index 87114134c7..7741dcce38 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-2.7.12.eb @@ -19,16 +19,13 @@ dependencies = [ ('Python', '2.7.12'), ('Qhull', '2015.2'), ('matplotlib', '1.5.3', versionsuffix), + ('Pillow', '3.4.2', versionsuffix), ] exts_list = [ ('networkx', '1.11', { 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], }), - ('Pillow', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pillow'], - 'modulename': 'PIL', - }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'modulename': 'skimage', diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb index bb4cf1ccf1..f0eef4a235 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.12.3-intel-2016b-Python-3.5.2.eb @@ -19,16 +19,13 @@ dependencies = [ ('Python', '3.5.2'), ('Qhull', '2015.2'), ('matplotlib', '1.5.3', versionsuffix), + ('Pillow', '3.4.2', versionsuffix), ] exts_list = [ ('networkx', '1.11', { 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], }), - ('Pillow', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pillow'], - 'modulename': 'PIL', - }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], 'modulename': 'skimage', -- GitLab From ac68a7ee260d0eb1e7ded3fd6dfc831b6daf790f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 15:04:04 +0200 Subject: [PATCH 678/701] add easyconfig ART-2016.06.05-intel-2016b.eb --- .../a/ART/ART-2016.06.05-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/ART/ART-2016.06.05-intel-2016b.eb diff --git a/easybuild/easyconfigs/a/ART/ART-2016.06.05-intel-2016b.eb b/easybuild/easyconfigs/a/ART/ART-2016.06.05-intel-2016b.eb new file mode 100644 index 0000000000..ac6f4932ff --- /dev/null +++ b/easybuild/easyconfigs/a/ART/ART-2016.06.05-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ART' +version = '2016.06.05' + +homepage = 'http://www.niehs.nih.gov/research/resources/software/biostatistics/art/' +description = "ART is a set of simulation tools to generate synthetic next-generation sequencing reads" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.niehs.nih.gov/research/resources/assets/docs/'] +sources = ['artsrcmountrainier%slinuxtgz.tgz' % ''.join(version.split('.'))] + +dependencies = [ + ('GSL', '2.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/aln2bed.pl', 'bin/art_454', 'bin/art_illumina', 'bin/art_profiler_454', + 'bin/art_profiler_illumina', 'bin/art_SOLiD', 'bin/combinedAvg.pl', 'bin/empDist.pl', + 'bin/fastqReadAvg.pl', 'bin/map2bed.pl', 'bin/summation.pl'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 84dcdf81d1103ff057405fb60ccec4a400bad055 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 20:11:50 +0200 Subject: [PATCH 679/701] move easyconfigs for deprecated iqacml & iiqmpi toolchains to archive --- .../{ => __archive__}/b/BLACS/BLACS-1.1-iiqmpi-3.3.0.eb | 0 .../{ => __archive__}/b/Bison/Bison-2.5-iqacml-3.7.3.eb | 0 .../{ => __archive__}/b/Bison/Bison-2.7-iqacml-3.7.3.eb | 0 .../{ => __archive__}/b/bzip2/bzip2-1.0.6-iqacml-3.7.3.eb | 0 .../{ => __archive__}/c/CBLAS/CBLAS-20110120-iqacml-3.7.3.eb | 0 .../{ => __archive__}/c/cURL/cURL-7.28.1-iqacml-3.7.3.eb | 0 .../{ => __archive__}/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb | 0 .../{ => __archive__}/e/ESMF/ESMF-6.1.1-iqacml-3.7.3.eb | 0 .../{ => __archive__}/f/FFTW/FFTW-3.3.3-iiqmpi-3.3.0.eb | 0 .../{ => __archive__}/f/FFTW/FFTW-3.3.3-iiqmpi-4.4.13.eb | 0 .../{ => __archive__}/f/flex/flex-2.5.35-iqacml-3.7.3.eb | 0 .../{ => __archive__}/f/flex/flex-2.5.37-iqacml-3.7.3.eb | 0 .../{ => __archive__}/f/flex/flex-2.5.37-iqacml-4.4.13.eb | 0 .../{ => __archive__}/f/freetype/freetype-2.4.11-iqacml-3.7.3.eb | 0 .../{ => __archive__}/g/GDAL/GDAL-1.9.2-iqacml-3.7.3.eb | 0 .../{ => __archive__}/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb | 0 .../{ => __archive__}/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb | 0 .../easyconfigs/{ => __archive__}/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb | 0 .../{ => __archive__}/h/HDF5/HDF5-1.8.10-patch1-iqacml-3.7.3.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iiqmpi/iiqmpi-3.3.0.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iiqmpi/iiqmpi-4.4.13.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iqacml/iqacml-3.7.3.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iqacml/iqacml-4.4.13.eb | 0 .../{ => __archive__}/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb | 0 .../{ => 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__archive__}/f/flex/flex-2.5.37-iqacml-4.4.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/freetype/freetype-2.4.11-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GDAL/GDAL-1.9.2-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HDF5/HDF5-1.8.10-patch1-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iiqmpi/iiqmpi-3.3.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iiqmpi/iiqmpi-4.4.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iqacml/iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iqacml/iqacml-4.4.13.eb (100%) rename easybuild/easyconfigs/{ => 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b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.5-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb b/easybuild/easyconfigs/__archive__/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb similarity index 100% rename from easybuild/easyconfigs/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb rename to easybuild/easyconfigs/__archive__/q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb b/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb similarity index 100% rename from easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb rename to easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb similarity index 100% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb rename to easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb similarity index 100% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb rename to easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/s/Szip/Szip-2.1-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/s/Szip/Szip-2.1-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/s/Szip/Szip-2.1-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb -- GitLab From fb4dce658d6dc84740228b0d0993dcff0186e528 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 20:11:57 +0200 Subject: [PATCH 680/701] ignore archived easyconfigs in test suite --- test/easyconfigs/easyconfigs.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 55faff811d..5901ae8d4c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -172,8 +172,8 @@ class EasyConfigTest(TestCase): easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$') topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) for (dirpath, _, filenames) in os.walk(topdir): - # ignore git/svn dirs - if '/.git/' in dirpath or '/.svn/' in dirpath: + # ignore git/svn dirs & archived easyconfigs + if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: continue # check whether list of .eb files is non-empty easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] @@ -313,6 +313,11 @@ def suite(): easyconfigs_path = get_paths_for('easyconfigs')[0] cnt = 0 for (subpath, _, specs) in os.walk(easyconfigs_path, topdown=True): + + # ignore archived easyconfigs + if '__archive__' in subpath: + continue + for spec in specs: if spec.endswith('.eb') and spec != 'TEMPLATE.eb': cnt += 1 -- GitLab From 6ed29e63f6dcb30eddff398cd3bf376ebebc11c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 20:37:34 +0200 Subject: [PATCH 681/701] add easyconfig CBLAS-20110120-foss-2016b.eb --- .../c/CBLAS/CBLAS-20110120-foss-2016b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-foss-2016b.eb b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-foss-2016b.eb new file mode 100644 index 0000000000..aadc3712b4 --- /dev/null +++ b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-foss-2016b.eb @@ -0,0 +1,22 @@ +name = 'CBLAS' +version = '20110120' + +homepage = 'http://www.netlib.org/blas/' +description = "C interface to the BLAS" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/blas/blast-forum/'] +sources = ['cblas.tgz'] + +patches = ['CBLAS_shared-lib.patch'] + +buildopts = 'all shared' + +# parallel build fails occasionally +parallel = 1 + +runtest = 'runtst' + +moduleclass = 'numlib' -- GitLab From d33fbb6dd48d6476dbd5d88978cb50937f91b158 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 19:35:03 +0200 Subject: [PATCH 682/701] move easyconfigs for deprecated iomkl toolchains to archive --- .../{ => __archive__}/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb | 0 .../{ => __archive__}/b/bzip2/bzip2-1.0.6-iomkl-4.6.13.eb | 0 .../{ => __archive__}/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb | 0 .../easyconfigs/{ => __archive__}/g/gzip/gzip-1.6-iomkl-6.6.2.eb | 0 .../easyconfigs/{ => __archive__}/h/HPL/HPL-2.0-iomkl-4.6.13.eb | 0 .../{ => __archive__}/i/imkl/imkl-10.3.12.361-iompi-4.6.13.eb | 0 .../{ => __archive__}/i/imkl/imkl-11.1.2.144-iompi-6.6.2.eb | 0 .../{ => __archive__}/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iomkl/iomkl-4.6.13.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iomkl/iomkl-6.6.2.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iompi/iompi-4.6.13.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iompi/iompi-6.6.2.eb | 0 .../easyconfigs/{ => __archive__}/i/iompi/iompi-6.6.4-no-OFED.eb | 0 easybuild/easyconfigs/{ => __archive__}/i/iompi/iompi-6.6.4.eb | 0 .../l/libreadline/libreadline-6.2-iomkl-4.6.13.eb | 0 .../{ => __archive__}/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 0 .../{ => __archive__}/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 0 .../p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb | 0 .../{ => __archive__}/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb | 0 19 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/bzip2/bzip2-1.0.6-iomkl-4.6.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gzip/gzip-1.6-iomkl-6.6.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.0-iomkl-4.6.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/imkl/imkl-10.3.12.361-iompi-4.6.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/imkl/imkl-11.1.2.144-iompi-6.6.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iomkl/iomkl-4.6.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iomkl/iomkl-6.6.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iompi/iompi-4.6.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iompi/iompi-6.6.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iompi/iompi-6.6.4-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/iompi/iompi-6.6.4.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/Python/Python-2.7.3-iomkl-4.6.13.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb (100%) diff --git a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-iomkl-4.6.13-single.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-iomkl-6.6.2.eb similarity index 100% rename from easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-iomkl-6.6.2.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.0-iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.0-iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-iompi-4.6.13.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-10.3.12.361-iompi-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-iompi-4.6.13.eb rename to easybuild/easyconfigs/__archive__/i/imkl/imkl-10.3.12.361-iompi-4.6.13.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-6.6.2.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-11.1.2.144-iompi-6.6.2.eb similarity index 100% rename from easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-6.6.2.eb rename to easybuild/easyconfigs/__archive__/i/imkl/imkl-11.1.2.144-iompi-6.6.2.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb similarity index 100% rename from easybuild/easyconfigs/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb rename to easybuild/easyconfigs/__archive__/i/imkl/imkl-11.1.4.211-iompi-6.6.4.eb diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/i/iomkl/iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/i/iomkl/iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/i/iomkl/iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-6.6.2.eb b/easybuild/easyconfigs/__archive__/i/iomkl/iomkl-6.6.2.eb similarity index 100% rename from easybuild/easyconfigs/i/iomkl/iomkl-6.6.2.eb rename to easybuild/easyconfigs/__archive__/i/iomkl/iomkl-6.6.2.eb diff --git a/easybuild/easyconfigs/i/iompi/iompi-4.6.13.eb b/easybuild/easyconfigs/__archive__/i/iompi/iompi-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/i/iompi/iompi-4.6.13.eb rename to easybuild/easyconfigs/__archive__/i/iompi/iompi-4.6.13.eb diff --git a/easybuild/easyconfigs/i/iompi/iompi-6.6.2.eb b/easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.2.eb similarity index 100% rename from easybuild/easyconfigs/i/iompi/iompi-6.6.2.eb rename to easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.2.eb diff --git a/easybuild/easyconfigs/i/iompi/iompi-6.6.4-no-OFED.eb b/easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.4-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/i/iompi/iompi-6.6.4-no-OFED.eb rename to easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.4-no-OFED.eb diff --git a/easybuild/easyconfigs/i/iompi/iompi-6.6.4.eb b/easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.4.eb similarity index 100% rename from easybuild/easyconfigs/i/iompi/iompi-6.6.4.eb rename to easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.4.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-iomkl-4.6.13.eb -- GitLab From 0f23f1dc68646a435b5bad2a271a5418e13efd5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 20:04:09 +0200 Subject: [PATCH 683/701] move easyconfigs for deprecated intel-para/gpsolf toolchains to archive --- .../{ => __archive__}/b/Bison/Bison-3.0.2-intel-para-2014.12.eb | 0 .../{ => __archive__}/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb | 0 .../{ => __archive__}/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb | 0 .../{ => __archive__}/f/flex/flex-2.5.39-intel-para-2014.12.eb | 0 .../easyconfigs/{ => __archive__}/g/gpsmpi/gpsmpi-2014.12.eb | 0 .../easyconfigs/{ => __archive__}/g/gpsolf/gpsolf-2014.12.eb | 0 .../easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-gpsolf-2014.12.eb | 0 .../{ => __archive__}/h/HPL/HPL-2.1-intel-para-2014.12.eb | 0 .../{ => __archive__}/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb | 0 .../{ => __archive__}/i/intel-para/intel-para-2014.12.eb | 0 .../easyconfigs/{ => __archive__}/i/ipsmpi/ipsmpi-2014.12.eb | 0 .../{ => __archive__}/l/Libint/Libint-1.1.4-intel-para-2014.12.eb | 0 .../{ => __archive__}/l/libxc/libxc-2.2.1-intel-para-2014.12.eb | 0 .../{ => __archive__}/m/M4/M4-1.4.17-intel-para-2014.12.eb | 0 ...ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb | 0 15 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/b/Bison/Bison-3.0.2-intel-para-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/flex/flex-2.5.39-intel-para-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gpsmpi/gpsmpi-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gpsolf/gpsolf-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-gpsolf-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-intel-para-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/intel-para/intel-para-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/ipsmpi/ipsmpi-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/Libint/Libint-1.1.4-intel-para-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libxc/libxc-2.2.1-intel-para-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/m/M4/M4-1.4.17-intel-para-2014.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/ScaLAPACK/ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb (100%) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb 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b/easybuild/easyconfigs/__archive__/f/flex/flex-2.5.39-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/f/flex/flex-2.5.39-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/g/gpsmpi/gpsmpi-2014.12.eb b/easybuild/easyconfigs/__archive__/g/gpsmpi/gpsmpi-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/g/gpsmpi/gpsmpi-2014.12.eb rename to easybuild/easyconfigs/__archive__/g/gpsmpi/gpsmpi-2014.12.eb diff --git a/easybuild/easyconfigs/g/gpsolf/gpsolf-2014.12.eb b/easybuild/easyconfigs/__archive__/g/gpsolf/gpsolf-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/g/gpsolf/gpsolf-2014.12.eb rename to easybuild/easyconfigs/__archive__/g/gpsolf/gpsolf-2014.12.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gpsolf-2014.12.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-gpsolf-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-gpsolf-2014.12.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-gpsolf-2014.12.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb rename to easybuild/easyconfigs/__archive__/i/imkl/imkl-11.2.1.133-ipsmpi-2014.12.eb diff --git a/easybuild/easyconfigs/i/intel-para/intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/i/intel-para/intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/i/intel-para/intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/i/intel-para/intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/i/ipsmpi/ipsmpi-2014.12.eb b/easybuild/easyconfigs/__archive__/i/ipsmpi/ipsmpi-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/i/ipsmpi/ipsmpi-2014.12.eb rename to easybuild/easyconfigs/__archive__/i/ipsmpi/ipsmpi-2014.12.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-2.2.1-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/l/libxc/libxc-2.2.1-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.17-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.17-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb similarity index 100% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gpsmpi-2014.12-OpenBLAS-0.2.12-LAPACK-3.5.0.eb -- GitLab From c14b3a6dd7680604cffd639163d9ee918c588c99 Mon 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a/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.5-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.0.10.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.0.10.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.0.10.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.0.10.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.3.5.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-ictce-6.3.5.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.3.5.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-ictce-6.3.5.eb diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/z/zsh/zsh-5.0.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/z/zsh/zsh-5.0.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-ictce-4.0.6.eb -- GitLab From d9d496bfc9186f24bfb2033fb0b994cfa777b279 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 21:15:48 +0200 Subject: [PATCH 685/701] also remove imkl easyconfigs that rely on deprecated iccifort toolchains --- .../i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb | 35 ------------------- .../i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb | 35 ------------------- 2 files changed, 70 deletions(-) delete mode 100644 easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb delete mode 100644 easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb deleted file mode 100644 index 4d5ef42fcf..0000000000 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-MVAPICH2-1.9.eb +++ /dev/null @@ -1,35 +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': ''} - -sources = ['l_mkl_%(version)s.tgz'] - -compver = '2011.13.367' -comp = ('iccifort', compver) - -# deps for interface build -mpi = 'MVAPICH2' -mpiver = '1.9' -versionsuffix = '-%s-%s' % (mpi, mpiver) - -dependencies = [ - ('icc', compver), - ('ifort', compver), - (mpi, mpiver, '', comp), -] - -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/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb deleted file mode 100644 index 2bd88ac625..0000000000 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361-OpenMPI-1.6.3.eb +++ /dev/null @@ -1,35 +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': ''} - -sources = ['l_mkl_%(version)s.tgz'] - -compver = '2011.13.367' -comp = ('iccifort', compver) - -# deps for interface build -mpi = 'OpenMPI' -mpiver = '1.6.3' -versionsuffix = '-%s-%s' % (mpi, mpiver) - -dependencies = [ - ('icc', compver), - ('ifort', compver), - (mpi, mpiver, '', comp), -] - -dontcreateinstalldir = 'True' - -interfaces = True - -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") - -moduleclass = 'numlib' -- GitLab From 9091b345d1ab7f50569da78faca94903b77ffa28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 21:19:52 +0200 Subject: [PATCH 686/701] move easyconfigs for deprecated goolfc toolchains to archive --- .../{ => __archive__}/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb | 0 .../{ => __archive__}/a/Automake/Automake-1.14-gcccuda-2.6.10.eb | 0 .../{ => __archive__}/c/CMake/CMake-2.8.12-goolfc-2.6.10.eb | 0 .../{ => __archive__}/c/CMake/CMake-2.8.4-goolfc-1.3.12.eb | 0 .../{ => __archive__}/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb | 0 .../{ => __archive__}/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb | 0 .../{ => __archive__}/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb | 0 .../g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb | 0 .../{ => __archive__}/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb | 0 .../g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb | 0 .../{ => __archive__}/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb | 0 .../easyconfigs/{ => __archive__}/g/GSL/GSL-1.16-goolfc-1.3.12.eb | 0 .../easyconfigs/{ => __archive__}/g/GSL/GSL-1.16-goolfc-2.6.10.eb | 0 .../easyconfigs/{ => __archive__}/g/gcccuda/gcccuda-2.6.10.eb | 0 easybuild/easyconfigs/{ => __archive__}/g/gompi/gompi-1.3.12.eb | 0 easybuild/easyconfigs/{ => __archive__}/g/gompic/gompic-2.6.10.eb | 0 easybuild/easyconfigs/{ => __archive__}/g/goolfc/goolfc-1.3.12.eb | 0 easybuild/easyconfigs/{ => __archive__}/g/goolfc/goolfc-1.4.10.eb | 0 easybuild/easyconfigs/{ => __archive__}/g/goolfc/goolfc-2.6.10.eb | 0 .../{ => __archive__}/g/gzip/gzip-1.6-goolfc-1.4.10.eb | 0 .../easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-goolfc-1.4.10.eb | 0 .../easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-goolfc-2.6.10.eb | 0 .../{ => __archive__}/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb | 0 .../{ => __archive__}/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb | 0 .../{ => __archive__}/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb | 0 .../{ => __archive__}/m/M4/M4-1.4.16-gcccuda-2.6.10.eb | 0 .../{ => __archive__}/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 0 .../{ => __archive__}/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 0 .../{ => __archive__}/n/netloc/netloc-0.5-gcccuda-2.6.10.eb | 0 .../o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb | 0 .../o/OpenBLAS/OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb | 0 .../{ => __archive__}/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 0 .../ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 0 .../ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb | 0 .../{ => __archive__}/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb | 0 .../{ => __archive__}/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb | 0 36 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/a/Automake/Automake-1.14-gcccuda-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CMake/CMake-2.8.12-goolfc-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CMake/CMake-2.8.4-goolfc-1.3.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GSL/GSL-1.16-goolfc-1.3.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GSL/GSL-1.16-goolfc-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gcccuda/gcccuda-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gompi/gompi-1.3.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gompic/gompic-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/goolfc/goolfc-1.3.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/goolfc/goolfc-1.4.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/goolfc/goolfc-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gzip/gzip-1.6-goolfc-1.4.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-goolfc-1.4.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-goolfc-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/m/M4/M4-1.4.16-gcccuda-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/netloc/netloc-0.5-gcccuda-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenBLAS/OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb (100%) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.14-gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/a/Automake/Automake-1.14-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/a/Automake/Automake-1.14-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolfc-2.6.10.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.12-goolfc-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolfc-2.6.10.eb rename to easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.12-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.4-goolfc-1.3.12.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.4-goolfc-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/c/CMake/CMake-2.8.4-goolfc-1.3.12.eb rename to easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.4-goolfc-1.3.12.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb rename to easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-gompi-1.3.12.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb 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easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-1.16-goolfc-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb rename to easybuild/easyconfigs/__archive__/g/GSL/GSL-1.16-goolfc-1.3.12.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-1.16-goolfc-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb rename to easybuild/easyconfigs/__archive__/g/GSL/GSL-1.16-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/g/gcccuda/gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/g/gcccuda/gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/g/gcccuda/gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.3.12.eb b/easybuild/easyconfigs/__archive__/g/gompi/gompi-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/g/gompi/gompi-1.3.12.eb rename to easybuild/easyconfigs/__archive__/g/gompi/gompi-1.3.12.eb diff --git a/easybuild/easyconfigs/g/gompic/gompic-2.6.10.eb b/easybuild/easyconfigs/__archive__/g/gompic/gompic-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/g/gompic/gompic-2.6.10.eb rename to easybuild/easyconfigs/__archive__/g/gompic/gompic-2.6.10.eb diff --git 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easybuild/easyconfigs/g/gzip/gzip-1.6-goolfc-1.4.10.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolfc-1.4.10.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolfc-1.4.10.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-goolfc-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-goolfc-1.4.10.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-goolfc-1.4.10.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolfc-2.6.10.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-goolfc-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-goolfc-2.6.10.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb rename to easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb rename to easybuild/easyconfigs/__archive__/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb rename to easybuild/easyconfigs/__archive__/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/n/netloc/netloc-0.5-gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/n/netloc/netloc-0.5-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb b/easybuild/easyconfigs/__archive__/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb rename to easybuild/easyconfigs/__archive__/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb -- GitLab From 0667c58a8165b450f8d945601672d1b88e25464c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 21:35:24 +0200 Subject: [PATCH 687/701] move easyconfigs for deprecated goolf/gompi toolchains to archive --- .../b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb | 0 .../b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb | 0 .../{ => __archive__}/b/bzip2/bzip2-1.0.6-gompi-1.4.12-no-OFED.eb | 0 .../c/CMake/CMake-2.8.10.2-gompi-1.4.12-no-OFED.eb | 0 .../{ => __archive__}/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb | 0 .../{ => __archive__}/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 0 .../{ => __archive__}/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb | 0 .../e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb | 0 .../{ => __archive__}/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb | 0 .../{ => __archive__}/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb | 0 .../g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb | 0 .../{ => __archive__}/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb | 0 .../{ => __archive__}/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb | 0 .../g/gettext/gettext-0.18.2-gompi-1.4.12-no-OFED.eb | 0 .../easyconfigs/{ => 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__archive__}/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GLib/GLib-2.34.3-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gettext/gettext-0.18.2-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gompi/gompi-1.4.10-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gompi/gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gompi/gompi-1.5.14-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/goolf/goolf-1.4.10-no-OFED.eb 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b/easybuild/easyconfigs/__archive__/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gompi-1.4.12-no-OFED.eb -- GitLab From f59a0553bd616c8f69d9a2a8435fe0a0e604e94d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 21:39:56 +0200 Subject: [PATCH 688/701] move easyconfigs for deprecated goalf toolchains to archive --- .../a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 0 .../a/ALADIN/ALADIN-36t1_op2bf1-goalf-1.1.0-no-OFED.eb | 0 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diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-goalf-1.5.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.8-goalf-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.8-goalf-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb -- GitLab From 3aee3411258232e0fc213a31cd8f5c6f70e957f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Oct 2016 21:46:52 +0200 Subject: [PATCH 689/701] move easyconfigs for deprecated gmvolf toolchains to archive --- .../{ => __archive__}/b/BLACS/BLACS-1.1-gmvapich2-1.6.7.eb | 0 .../{ => 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__archive__}/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/flex/flex-2.5.35-gmvapich2-1.6.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gettext/gettext-0.18.2-gmvolf-1.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gettext/gettext-0.18.2-gmvolf-1.7.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/git/git-1.8.2-gmvolf-1.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/git/git-1.8.2-gmvolf-1.7.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmvapich2/gmvapich2-1.1.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmvapich2/gmvapich2-1.6.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmvapich2/gmvapich2-1.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmvapich2/gmvapich2-1.7.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmvapich2/gmvapich2-1.7.20.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmvapich2/gmvapich2-1.7.9a2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmvolf/gmvolf-1.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmvolf/gmvolf-1.7.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12-Python-2.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/m/Mercurial/Mercurial-2.5.2-gmvolf-1.7.12rc1-Python-2.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12rc1-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => 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a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvolf-1.7.12.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvolf-1.7.12.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvolf-1.7.12.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvolf-1.7.12.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvolf-1.7.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvolf-1.7.12rc1.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmvolf-1.7.12rc1.eb -- GitLab From 6bed37ff6c66f579fba69746a855678999d7f1ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Oct 2016 08:41:32 +0200 Subject: [PATCH 690/701] add easyconfig IronPython-2.7-intel-2016b.eb, add easyconfig Mono-2.10.6-intel-2016b.eb, add easyconfig MyMediaLite-3.10-intel-2016b.eb --- .../IronPython/IronPython-2.7-intel-2016b.eb | 16 +++++++++++ .../m/Mono/Mono-2.10.6-intel-2016b.eb | 28 +++++++++++++++++++ .../MyMediaLite-3.10-intel-2016b.eb | 14 ++++++++++ 3 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/i/IronPython/IronPython-2.7-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-intel-2016b.eb diff --git a/easybuild/easyconfigs/i/IronPython/IronPython-2.7-intel-2016b.eb b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-intel-2016b.eb new file mode 100644 index 0000000000..b0645a78ef --- /dev/null +++ b/easybuild/easyconfigs/i/IronPython/IronPython-2.7-intel-2016b.eb @@ -0,0 +1,16 @@ +name = 'IronPython' +version = '2.7' + +homepage = 'http://ironpython.net/' +description = """IronPython is an open-source implementation of the Python programming language + which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and +Python libraries, and other .NET languages can use Python code just as easily.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/IronLanguages/main/archive/'] +sources = ['ipy-%(version)s.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb new file mode 100644 index 0000000000..365455df1b --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb @@ -0,0 +1,28 @@ +name = 'Mono' +version = '2.10.6' + +homepage = 'http://mono-framework.com' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# Mono required Mono to build, so there are a couple of options: +# 1) provide Mono RPMs in sources, the Mono easyblock will use them to make a tmp Mono install +# 2) assume a Mono version is available system-wide (assert using e.g. "osdependencies = ['mono-core']") +# 3) specify an already available Mono module as build dep, e.g. "builddependencies = [('Mono', '2.10.6')] + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [ + SOURCELOWER_TAR_BZ2, + # Mono requires Mono to build, so provide RPMs so Mono can be bootstrapped + 'libgdiplus-2.4.2-2.el5.kb.x86_64.rpm', + 'mono-core-2.4.2.3-2.el5.kb.x86_64.rpm', +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('gettext', '0.19.8'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-intel-2016b.eb b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-intel-2016b.eb new file mode 100644 index 0000000000..75f50aa79e --- /dev/null +++ b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.10-intel-2016b.eb @@ -0,0 +1,14 @@ +name = 'MyMediaLite' +version = '3.10' + +homepage = 'http://www.ismll.uni-hildesheim.de/mymedialite/' +description = """MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.mymedialite.net/download/'] +sources = ['%(name)s-%(version)s.src.tar.gz'] + +dependencies = [('Mono', '2.10.6')] + +moduleclass = 'lib' -- GitLab From 9718e1f97a0f6c73aad408de5f6b3f31002e5cc4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Oct 2016 09:06:05 +0200 Subject: [PATCH 691/701] move easyconfigs for deprecated gimkl 1.5.9 toolchain to archive --- easybuild/easyconfigs/{ => __archive__}/g/gimkl/gimkl-1.5.9.eb | 0 easybuild/easyconfigs/{ => __archive__}/g/gimpi/gimpi-1.5.9.eb | 0 .../easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-gimkl-1.5.9.eb | 0 .../{ => __archive__}/i/imkl/imkl-11.1.2.144-gimpi-1.5.9.eb | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/g/gimkl/gimkl-1.5.9.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gimpi/gimpi-1.5.9.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-gimkl-1.5.9.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/imkl/imkl-11.1.2.144-gimpi-1.5.9.eb (100%) diff --git a/easybuild/easyconfigs/g/gimkl/gimkl-1.5.9.eb b/easybuild/easyconfigs/__archive__/g/gimkl/gimkl-1.5.9.eb similarity index 100% rename from easybuild/easyconfigs/g/gimkl/gimkl-1.5.9.eb rename to easybuild/easyconfigs/__archive__/g/gimkl/gimkl-1.5.9.eb diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-1.5.9.eb b/easybuild/easyconfigs/__archive__/g/gimpi/gimpi-1.5.9.eb similarity index 100% rename from easybuild/easyconfigs/g/gimpi/gimpi-1.5.9.eb rename to easybuild/easyconfigs/__archive__/g/gimpi/gimpi-1.5.9.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-1.5.9.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-gimkl-1.5.9.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-1.5.9.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-gimkl-1.5.9.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-gimpi-1.5.9.eb b/easybuild/easyconfigs/__archive__/i/imkl/imkl-11.1.2.144-gimpi-1.5.9.eb similarity index 100% rename from easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-gimpi-1.5.9.eb rename to easybuild/easyconfigs/__archive__/i/imkl/imkl-11.1.2.144-gimpi-1.5.9.eb -- GitLab From 4b026f0a2a0ff28eae19a1b8b5b84b2fa56034a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Oct 2016 09:12:31 +0200 Subject: [PATCH 692/701] move easyconfigs for deprecated Clang-based toolchains to archive --- .../{ => __archive__}/b/Bison/Bison-2.7-ClangGCC-1.1.3.eb | 0 .../{ => __archive__}/b/Bison/Bison-2.7-ClangGCC-1.2.3.eb | 0 .../{ => __archive__}/b/bzip2/bzip2-1.0.6-cgmpolf-1.1.6.eb | 0 .../{ => __archive__}/b/bzip2/bzip2-1.0.6-cgmvolf-1.1.12rc1.eb | 0 .../{ => __archive__}/b/bzip2/bzip2-1.0.6-cgmvolf-1.2.7.eb | 0 .../{ => __archive__}/b/bzip2/bzip2-1.0.6-cgoolf-1.1.7.eb | 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.../v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb | 0 .../{ => __archive__}/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb | 0 .../{ => __archive__}/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb | 0 .../{ => __archive__}/z/zlib/zlib-1.2.7-cgmpolf-1.1.6.eb | 0 .../{ => __archive__}/z/zlib/zlib-1.2.7-cgmvolf-1.1.12rc1.eb | 0 .../{ => __archive__}/z/zlib/zlib-1.2.7-cgmvolf-1.2.7.eb | 0 .../{ => __archive__}/z/zlib/zlib-1.2.7-cgoolf-1.1.7.eb | 0 90 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/b/Bison/Bison-2.7-ClangGCC-1.1.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/Bison/Bison-2.7-ClangGCC-1.2.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/bzip2/bzip2-1.0.6-cgmpolf-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/bzip2/bzip2-1.0.6-cgmvolf-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/bzip2/bzip2-1.0.6-cgmvolf-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/bzip2/bzip2-1.0.6-cgoolf-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/ClangGCC/ClangGCC-1.1.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/ClangGCC/ClangGCC-1.2.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/ClangGCC/ClangGCC-1.3.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cURL/cURL-7.29.0-cgmpolf-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cURL/cURL-7.29.0-cgmvolf-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cURL/cURL-7.29.0-cgmvolf-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cURL/cURL-7.29.0-cgoolf-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cgmpich/cgmpich-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cgmpolf/cgmpolf-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cgmvapich2/cgmvapich2-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cgmvapich2/cgmvapich2-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cgmvolf/cgmvolf-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cgmvolf/cgmvolf-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cgompi/cgompi-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/cgoolf/cgoolf-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/e/expat/expat-2.1.0-cgoolf-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.3-cgmpich-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.3-cgmvapich2-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.3-cgmvapich2-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.3-cgompi-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gettext/gettext-0.18.2-cgoolf-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/git/git-1.8.2-cgmpolf-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/git/git-1.8.2-cgmvolf-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/git/git-1.8.2-cgmvolf-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/git/git-1.8.2-cgoolf-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gzip/gzip-1.5-cgoolf-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.0-cgmpolf-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.0-cgmvolf-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.0-cgmvolf-1.2.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.0-cgoolf-1.1.7.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/hwloc/hwloc-1.6.2-ClangGCC-1.1.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb (100%) 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easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.2.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.2.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.2.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.2.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmpolf-1.1.6.eb similarity index 100% rename from easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmpolf-1.1.6.eb rename to easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmpolf-1.1.6.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb rename to easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb similarity index 100% rename from easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb rename to easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb similarity index 100% rename from easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb rename to easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmpolf-1.1.6.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmpolf-1.1.6.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmpolf-1.1.6.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmvolf-1.1.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmvolf-1.1.12rc1.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmvolf-1.1.12rc1.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmvolf-1.2.7.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgmvolf-1.2.7.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgmvolf-1.2.7.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgoolf-1.1.7.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-cgoolf-1.1.7.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-cgoolf-1.1.7.eb -- GitLab From b10911a757d3f4f00d341725cbf673e227dbe562 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Oct 2016 09:23:12 +0200 Subject: [PATCH 693/701] move easyconfigs for deprecated gmacml and gmpolf toolchains to archive --- .../{ => __archive__}/b/BLACS/BLACS-1.1-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/b/Bison/Bison-2.5-gmacml-1.7.0.eb | 0 .../{ => __archive__}/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/c/CMake/CMake-2.8.10.2-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/c/CMake/CMake-2.8.4-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb | 0 .../easyconfigs/{ => __archive__}/d/DB/DB-5.3.28-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb | 0 .../{ => __archive__}/f/flex/flex-2.5.35-gmacml-1.7.0.eb | 0 .../{ => __archive__}/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb | 0 .../g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb | 0 .../{ => __archive__}/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb | 0 .../{ => __archive__}/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb | 0 easybuild/easyconfigs/{ => __archive__}/g/gmacml/gmacml-1.7.0.eb | 0 easybuild/easyconfigs/{ => __archive__}/g/gmpich/gmpich-1.4.8.eb | 0 easybuild/easyconfigs/{ => __archive__}/g/gmpolf/gmpolf-1.4.8.eb | 0 .../easyconfigs/{ => __archive__}/g/gzip/gzip-1.5-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb | 0 .../easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/l/LAPACK/LAPACK-3.4.2-gmpich-1.4.8.eb | 0 .../{ => __archive__}/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb | 0 .../{ => __archive__}/l/libffi/libffi-3.0.11-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/l/libffi/libffi-3.0.13-gmpolf-1.4.8.eb | 0 .../l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb | 0 .../{ => __archive__}/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb | 0 .../easyconfigs/{ => __archive__}/m/M4/M4-1.4.16-gmacml-1.7.0.eb | 0 .../{ => __archive__}/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb | 0 .../{ => __archive__}/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 0 .../o/OpenBLAS/OpenBLAS-0.2.6-gmpich-1.4.8-LAPACK-3.4.2.eb | 0 .../{ => __archive__}/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 0 .../easyconfigs/{ => __archive__}/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb | 0 .../s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb | 0 .../ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 0 .../ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb | 0 .../s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb | 0 .../easyconfigs/{ => __archive__}/s/Szip/Szip-2.1-gmpolf-1.4.8.eb | 0 .../{ => __archive__}/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb | 0 47 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/b/BLACS/BLACS-1.1-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/Bison/Bison-2.5-gmacml-1.7.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CMake/CMake-2.8.10.2-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CMake/CMake-2.8.4-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/d/DB/DB-5.3.28-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/f/flex/flex-2.5.35-gmacml-1.7.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmacml/gmacml-1.7.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmpich/gmpich-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gmpolf/gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gzip/gzip-1.5-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.1-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/LAPACK/LAPACK-3.4.2-gmpich-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libffi/libffi-3.0.11-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libffi/libffi-3.0.13-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/m/M4/M4-1.4.16-gmacml-1.7.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenBLAS/OpenBLAS-0.2.6-gmpich-1.4.8-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/Python/Python-2.7.3-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/Szip/Szip-2.1-gmpolf-1.4.8.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb (100%) diff --git a/easybuild/easyconfigs/b/BLACS/BLACS-1.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/b/BLACS/BLACS-1.1-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/b/BLACS/BLACS-1.1-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/b/BLACS/BLACS-1.1-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-gmacml-1.7.0.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-2.5-gmacml-1.7.0.eb similarity index 100% rename from easybuild/easyconfigs/b/Bison/Bison-2.5-gmacml-1.7.0.eb rename to easybuild/easyconfigs/__archive__/b/Bison/Bison-2.5-gmacml-1.7.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.10.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.10.2-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/c/CMake/CMake-2.8.10.2-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.10.2-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.4-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.4-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/c/CMake/CMake-2.8.4-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.4-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb similarity index 100% rename from easybuild/easyconfigs/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb rename to easybuild/easyconfigs/__archive__/c/CP2K/CP2K-20111205-gmacml-1.7.0-libsmm.eb diff --git a/easybuild/easyconfigs/d/DB/DB-5.3.28-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/d/DB/DB-5.3.28-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/d/DB/DB-5.3.28-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/d/DB/DB-5.3.28-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-gmpich-1.4.8.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.35-gmacml-1.7.0.eb b/easybuild/easyconfigs/__archive__/f/flex/flex-2.5.35-gmacml-1.7.0.eb similarity index 100% rename from easybuild/easyconfigs/f/flex/flex-2.5.35-gmacml-1.7.0.eb rename to easybuild/easyconfigs/__archive__/f/flex/flex-2.5.35-gmacml-1.7.0.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/g/GLib/GLib-2.34.3-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/g/gmacml/gmacml-1.7.0.eb b/easybuild/easyconfigs/__archive__/g/gmacml/gmacml-1.7.0.eb similarity index 100% rename from easybuild/easyconfigs/g/gmacml/gmacml-1.7.0.eb rename to easybuild/easyconfigs/__archive__/g/gmacml/gmacml-1.7.0.eb diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-1.4.8.eb b/easybuild/easyconfigs/__archive__/g/gmpich/gmpich-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/g/gmpich/gmpich-1.4.8.eb rename to easybuild/easyconfigs/__archive__/g/gmpich/gmpich-1.4.8.eb diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/g/gmpolf/gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/g/gmpolf/gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/g/gmpolf/gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/g/gzip/gzip-1.5-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.1-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gmpich-1.4.8.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gmpich-1.4.8.eb similarity index 100% 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easybuild/easyconfigs/l/libffi/libffi-3.0.13-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb b/easybuild/easyconfigs/__archive__/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb similarity index 100% rename from easybuild/easyconfigs/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb rename to easybuild/easyconfigs/__archive__/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-gmacml-1.7.0.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-gmacml-1.7.0.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-gmacml-1.7.0.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-gmacml-1.7.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb similarity index 100% rename from easybuild/easyconfigs/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb rename to easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmpich-1.4.8-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.2.6-gmpich-1.4.8-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmpich-1.4.8-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/o/OpenBLAS/OpenBLAS-0.2.6-gmpich-1.4.8-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/o/OpenSSL/OpenSSL-1.0.0-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-3.2.0-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/ParaView/ParaView-4.0.1-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/ParaView/ParaView-4.1.0-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/Python/Python-2.7.3-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb similarity index 100% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/s/ScientificPython/ScientificPython-2.8-gmpolf-1.4.8-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb b/easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb similarity index 100% rename from easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb rename to easybuild/easyconfigs/__archive__/s/SuiteSparse/SuiteSparse-3.7.0-gmpolf-1.4.8-withparmetis.eb diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/s/Szip/Szip-2.1-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/s/Szip/Szip-2.1-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/s/Szip/Szip-2.1-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.7-gmpolf-1.4.8.eb -- GitLab From 001504eca3a7df5185610b9b3cb6c88fe843a5d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Oct 2016 09:41:16 +0200 Subject: [PATCH 694/701] add easyconfig BLACS-1.1-gmvapich2-2016a.eb --- .../b/BLACS/BLACS-1.1-gmvapich2-2016a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLACS/BLACS-1.1-gmvapich2-2016a.eb diff --git a/easybuild/easyconfigs/b/BLACS/BLACS-1.1-gmvapich2-2016a.eb b/easybuild/easyconfigs/b/BLACS/BLACS-1.1-gmvapich2-2016a.eb new file mode 100644 index 0000000000..714b83985a --- /dev/null +++ b/easybuild/easyconfigs/b/BLACS/BLACS-1.1-gmvapich2-2016a.eb @@ -0,0 +1,24 @@ +name = 'BLACS' +version = '1.1' + +homepage = 'http://www.netlib.org/blacs/' +description = """The BLACS (Basic Linear Algebra Communication Subprograms) project is + an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface + that may be implemented efficiently and uniformly across a large range of distributed memory platforms.""" + +toolchain = {'name': 'gmvapich2', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [ + 'mpiblacs.tgz', + 'mpiblacs-patch03.tgz', +] +checksums = [ + '28ae5b91b3193402fe1ae8d06adcf500', + '48fdf5e4ef6cf53daec9eeef40498a8b', +] + +patches = ['bmake.mpi.patch'] + +moduleclass = 'numlib' -- GitLab From 0fe8de149c887d037f548d6f7a9bc5873227952d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Oct 2016 11:05:13 +0200 Subject: [PATCH 695/701] move back easyconfigs required for (non-deprecated) gmvolf/1.7.20 toolchain --- .../{__archive__ => }/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb | 0 .../easyconfigs/{__archive__ => }/g/gmvapich2/gmvapich2-1.7.20.eb | 0 ...aLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{__archive__ => }/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb (100%) rename easybuild/easyconfigs/{__archive__ => }/g/gmvapich2/gmvapich2-1.7.20.eb (100%) rename easybuild/easyconfigs/{__archive__ => }/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb (100%) diff --git a/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb diff --git a/easybuild/easyconfigs/__archive__/g/gmvapich2/gmvapich2-1.7.20.eb b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/g/gmvapich2/gmvapich2-1.7.20.eb rename to easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb diff --git a/easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb -- GitLab From 49a5a0ad28ee85aff035b3d86560a3b2a47755ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Oct 2016 12:27:22 +0200 Subject: [PATCH 696/701] add easyconfig MUST-1.2.0-goolf-1.5.14.eb, add easyconfig PnMPI-1.2.0-goolf-1.5.14.eb, add easyconfig GTI-1.2.0-goolf-1.5.14.eb --- .../g/GTI/GTI-1.2.0-goolf-1.5.14.eb | 38 ++++++++++++++++++ .../m/MUST/MUST-1.2.0-goolf-1.5.14.eb | 39 +++++++++++++++++++ .../p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb | 35 +++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..d2f8ea38ad --- /dev/null +++ b/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb @@ -0,0 +1,38 @@ +# 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 = 'CMakeMake' + +name = 'GTI' +version = '1.2.0' + +homepage = 'http://www.tu-dresden.de/zih/must/' +description = """A Generic Tools Infrastructure for Event-Based Tools in Parallel Systems.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +# http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/gti-release-1.2.0.tar.gz +source_urls = ['http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/'] +sources = ['%(namelower)s-release-%(version)s.tar.gz'] + +patches = ['GTI-%(version)s-missing-unistd.patch'] + +dependencies = [('PnMPI', '1.2.0')] + +builddependencies = [('CMake', '3.0.2')] + +configopts = '-DCMAKE_BUILD_TYPE=Release -DPnMPI_INSTALL_PREFIX=${EBROOTPNMPI}' +buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' + +sanity_check_paths = { + 'files': ["bin/weaver", "include/I_Profiler.h"], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..a3e8ea9b64 --- /dev/null +++ b/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'CMakeMake' + +name = 'MUST' +version = '1.2.0' + +homepage = 'http://www.tu-dresden.de/zih/must/' +description = """MUST detects usage errors of the Message Passing Interface (MPI) and reports them + to the user. As MPI calls are complex and usage errors common, this functionality is extremely helpful + for application developers that want to develop correct MPI applications. This includes errors that + already manifest --segmentation faults or incorrect results -- as well as many errors that are not + visible to the application developer or do not manifest on a certain system or MPI implementation.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +# http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/must-release-1.2.0.tar.gz +source_urls = ['http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/'] +sources = ['%(namelower)s-release-%(version)s.tar.gz'] + +dependencies = [('GTI', '1.2.0')] + +builddependencies = [('CMake', '3.0.2')] + +configopts = ' -DCMAKE_BUILD_TYPE=Release -DGTI_INSTALL_PREFIX=${EBROOTGTI}' + +sanity_check_paths = { + 'files': ['bin/mustrun', 'include/mustConfig.h'], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..30ff748dc8 --- /dev/null +++ b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb @@ -0,0 +1,35 @@ +# 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 = 'CMakeMake' + +name = 'PnMPI' +version = '1.2.0' + +homepage = 'https://scalability.llnl.gov/pnmpi/' +description = """MPI Tool Virtualization and Interoperability library.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +# http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/pnmpi-for-gti-1.2.0.tar.gz +source_urls = ['http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/must/files/'] +sources = ['%(namelower)s-for-gti-%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.0.2')] + +configopts = ' -DCMAKE_BUILD_TYPE=Release -DBFD_FOUND=False -DPNMPI_HAVE_BFD=False' + +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/pnmpi-patch", "include/pnmpi.h", "lib/libpnmpi.a"], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From 27424b4b5054ac1de02e22eb50501be650c7fd7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Oct 2016 18:40:51 +0200 Subject: [PATCH 697/701] add easyconfig TAU-2.22.2-goolf-1.5.14.eb, add easyconfig VampirTrace-5.14.4-goolf-1.5.14.eb --- .../c/Cube/Cube-4.2-goolf-1.5.14.eb | 56 +++++++++++++++++++ .../o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb | 31 ++++++++++ .../o/OTF/OTF-1.12.4-goolf-1.5.14.eb | 34 +++++++++++ .../p/PDT/PDT-3.19-goolf-1.5.14.eb | 32 +++++++++++ .../s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb | 39 +++++++++++++ .../t/TAU/TAU-2.22.2-goolf-1.5.14.eb | 35 ++++++++++++ .../VampirTrace-5.14.4-goolf-1.5.14.eb | 50 +++++++++++++++++ 7 files changed, 277 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb new file mode 100644 index 0000000000..94f4a3ca61 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb @@ -0,0 +1,56 @@ +## +# 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 = '4.2' + +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': 'goolf', 'version': '1.5.14'} + +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-%(version)s_fix-Qt-version-check.patch', + 'Cube-%(version)s_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', '4.8.6')] + +# 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', 'lib64/libcube4.a'), + ('lib/libcube4.%s' % SHLIB_EXT, 'lib64/libcube4.%s' % SHLIB_EXT)], + 'dirs': ['include/cube', 'include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..d50dab2154 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-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 = 'ConfigureMake' + +name = 'OPARI2' +version = '1.1.1' + +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/o/OTF/OTF-1.12.4-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb new file mode 100644 index 0000000000..831526692c --- /dev/null +++ b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb @@ -0,0 +1,34 @@ +# 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 = 'OTF' +version = '1.12.4' + +homepage = 'http://www.tu-dresden.de/zih/otf/' +description = """The Open Trace Format is a highly scalable, memory efficient event + trace data format plus support library. It is the standard trace format + for Vampir, and is open for other tools. [NOW OBSOLETE: use OTF2]""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.4salmon.tar.gz +sources = ['%(name)s-%(version)ssalmon.tar.gz'] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get='] + +# name change in version 1.12.3: "open-trace-format" was "otf" in older versions +# "open-trace-format" => "otf" for versions until 1.12.2 +sanity_check_paths = { + 'files': ['bin/otfconfig', 'include/open-trace-format/otf.h', + # note by Bernd Mohr: on some systems libraries end up in lib/ + ('lib64/libopen-trace-format.a', 'lib/libopen-trace-format.a')], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb new file mode 100644 index 0000000000..48f0570291 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb @@ -0,0 +1,32 @@ +## +# 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/ +## + +name = 'PDT' +version = '3.19' + +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'} + +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..df0333c95e --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.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/ +## +name = 'Score-P' +version = '1.2.1' + +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 = [ + ('Cube', '4.2'), + ('OPARI2', '1.1.1'), + ('OTF2', '1.2.1'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), +] + +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' diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb new file mode 100644 index 0000000000..2f2888a832 --- /dev/null +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb @@ -0,0 +1,35 @@ +# 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/ +## +name = 'TAU' +version = '2.22.2' + +homepage = 'http://tau.uoregon.edu' +description = """The TAU Performance System is a portable profiling and tracing toolkit + for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('OTF', '1.12.4'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), + ('Score-P', '1.2.1'), + # obsolete backends, use Score-P instead + #('Scalasca', '1.4.3'), + #('VampirTrace', '5.14.4'), +] + +# scalasca and vampirtrace backends are deprecated +extra_backends = ['scorep'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb new file mode 100644 index 0000000000..722868d4b7 --- /dev/null +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.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 = 'VampirTrace' +version = '5.14.4' + +homepage = 'http:/www.tu-dresden.de/zih/vampirtrace/' +description = """VampirTrace is an open source library that allows detailed logging of program + execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads).""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get='] + +dependencies = [ + ('OTF', '1.12.4'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), +] + +configopts = 'MPIFC="$MPIF90"' + +# MPI suite should always be specified -- MUCH quicker and SAVER than autodetect +# note: these options are toolchain specific! +configopts += " --with-openmpi --enable-compinst=gnu" + +configopts += " --with-papi-dir=${EBROOTPAPI}" +configopts += " --with-extern-otf-dir=${EBROOTOTF}" +configopts += " --with-tau-instrumentor=${EBROOTPDT}/x86_64/bin/tau_instrumentor" +configopts += " --with-pdt-cparse=${EBROOTPDT}/x86_64/bin/cparse" +configopts += " --with-pdt-cxxparse=${EBROOTPDT}/x86_64/bin/cxxparse" +configopts += " --with-pdt-fparse=${EBROOTPDT}/x86_64/bin/gfparse" +# VamoirTrace does also support CUDA measurements - not yet tested +# configopts += " --with-cuda-dir=${CUDADIR}" + +sanity_check_paths = { + 'files': ['bin/vtcc', 'include/vampirtrace/vt_user.h', ('lib/libvt.a', 'lib64/libvt.a')], + 'dirs': [] +} + +moduleclass = 'perf' -- GitLab From 68dcd038fb91ea196781e750d67f8c3a49bbe109 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Oct 2016 20:07:20 +0200 Subject: [PATCH 698/701] add easyconfig ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb --- ...TLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb diff --git a/easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb new file mode 100644 index 0000000000..5d4cb8e99d --- /dev/null +++ b/easybuild/easyconfigs/a/ATLAS/ATLAS-3.10.2-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -0,0 +1,36 @@ +name = 'ATLAS' +version = '3.10.2' + +homepage = 'http://math-atlas.sourceforge.net' +description = """ATLAS (Automatically Tuned Linear Algebra Software) is the application of + the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis + on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear + algebra kernel library.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +toolchainopts = {'pic': True} + +lapackver = '3.6.1' +versionsuffix = '-LAPACK-%s' % lapackver + +source_urls = [ + ('http://sourceforge.net/projects/math-atlas/files/Stable/%(version)s', 'download'), + 'http://www.netlib.org/lapack/', +] +sources = [ + '%(namelower)s%(version)s.tar.bz2', + 'lapack-%s.tgz' % lapackver, +] + +# build full LAPACK library with supplied netlib LAPACK +full_lapack = True + +# fix for http://math-atlas.sourceforge.net/errata.html#sharedProbe +configopts = "-Ss f77lib '-L$(EBROOTGCC)/lib64 -lgfortran'" + +# ignore check done by ATLAS for CPU throttling; +# you should set this to False (or remove it) +# and disable CPU throttling (requires root privileges) if you can +ignorethrottling = True + +moduleclass = 'numlib' -- GitLab From 0e5065cb31ce49db06316845a29ac2b702c802d5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 30 Oct 2016 20:21:11 +0100 Subject: [PATCH 699/701] add easyconfig BamTools-2.4.0-foss-2016b.eb, add easyconfig CMake-3.4.3-foss-2016b.eb --- .../b/BamTools/BamTools-2.4.0-foss-2016b.eb | 31 +++++++++++++++++++ .../c/CMake/CMake-3.4.3-foss-2016b.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb new file mode 100644 index 0000000000..b1a2aa0cf6 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , George Tsouloupas +# License:: MIT/GPL +# +## + +name = 'BamTools' +version = '2.4.0' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = """BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/pezmaster31/bamtools/archive'] + +builddependencies = [('CMake', '3.4.3')] + +files_to_copy = ["bin", "lib", "include", "docs", "LICENSE", "README"] + +sanity_check_paths = { + 'files': ["bin/bamtools", "include/shared/bamtools_global.h", "lib/libbamtools.a", + "lib/libbamtools.so", "lib/libbamtools-utils.a", "lib/libjsoncpp.a"], + 'dirs': ["include/api", "docs"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb new file mode 100644 index 0000000000..cfb29da8c6 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.3' + +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': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # 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', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 81f1ceb234ea07b29425d3d18d979ee6a5cf63e5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 30 Oct 2016 20:43:56 +0100 Subject: [PATCH 700/701] add easyconfig Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb --- .../Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9a77cac29a --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'Bundle' + +name = 'Pysam' +version = '0.9.1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +parallel = 1 + +dependencies = [ + ('Python', '2.7.12'), + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('Cython', '0.25.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('pysam', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pysam-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], +} + +moduleclass = 'bio' -- GitLab From 73985dfc58fb63c22f7291be6cb3be7362630f2d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 30 Oct 2016 20:58:39 +0100 Subject: [PATCH 701/701] add easyconfig libpng-1.6.26-foss-2016b.eb --- .../l/libpng/libpng-1.6.26-foss-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.26-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.26-foss-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.26-foss-2016b.eb new file mode 100644 index 0000000000..83dd651c2b --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.26-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.26' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' -- GitLab