From 46c14aa7795447b96c6714043a15b2a03210f153 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 22 Mar 2016 12:09:24 +0100 Subject: [PATCH 001/350] {math}[foss-2016a] Octave 4.0.0 (REVIEW) --- .../a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb | 25 ++++++++ .../o/Octave/Octave-4.0.0-foss-2016a.eb | 58 +++++++++++++++++++ .../q/Qhull/Qhull-2015.2-foss-2016a.eb | 37 ++++++++++++ ...uiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb | 24 ++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2015.2-foss-2016a.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb new file mode 100644 index 0000000000..939e49dbc0 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.3.0' + +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': 'foss', 'version': '2016a'} +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' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb new file mode 100644 index 0000000000..bf4776d474 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.0.0' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXft', '2.3.2'), + ('PCRE', '8.38'), + ('ncurses', '6.0'), + ('libreadline', '6.3'), + ('arpack-ng', '3.3.0'), + ('cURL', '7.47.0'), + ('FLTK', '1.3.3'), + ('fontconfig', '2.11.94'), + ('freetype', '2.6.2'), + ('GLPK', '4.58'), + ('GL2PS', '1.3.9'), + ('gnuplot', '5.0.3'), + ('Java', '1.8.0_72', '', True), + ('zlib', '1.2.8'), + ('Mesa', '11.1.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt', '4.8.7'), + ('HDF5', '1.8.16', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.1', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.23'), +] + +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' 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' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000..7b07d451fc --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb @@ -0,0 +1,24 @@ +name = 'SuiteSparse' +version = '4.5.1' + +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] + +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] + +preconfigopts = 'LAPACK="$LIBLAPACK" ' +prebuildopts = 'LAPACK="$LIBLAPACK" ' +preinstallopts = 'LAPACK="$LIBLAPACK" ' + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From 071a61763eb77f420ab71153d85c722f878b8ede Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 13 May 2016 12:37:09 +0200 Subject: [PATCH 002/350] remove pre*=LAPACK="$LIBLAPACK" option --- .../s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb index 7b07d451fc..6a80824b3c 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.1-foss-2016a-METIS-5.1.0.eb @@ -15,10 +15,6 @@ metis_ver = '5.1.0' versionsuffix = '-%s-%s' % (metis, metis_ver) dependencies = [(metis, metis_ver)] -preconfigopts = 'LAPACK="$LIBLAPACK" ' -prebuildopts = 'LAPACK="$LIBLAPACK" ' -preinstallopts = 'LAPACK="$LIBLAPACK" ' - maxparallel = 1 moduleclass = 'numlib' -- GitLab From 58fa2bf2a417c3407aff5c7d6a34b02589753a67 Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Fri, 20 May 2016 13:01:44 -0400 Subject: [PATCH 003/350] Create x264-20160304-goolf-1.7.20.eb --- .../x/x264/x264-20160304-goolf-1.7.20.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb new file mode 100644 index 0000000000..de24dff5a1 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160304' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://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' -- GitLab From 4c9d1810e9ae2837506c88c385c52b834c926d32 Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Fri, 20 May 2016 13:05:20 -0400 Subject: [PATCH 004/350] Create x265-1.9-goolf-1.7.20.eb for goolf --- .../easyconfigs/x/x265-1.9-goolf-1.7.20.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/x/x265-1.9-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/x/x265-1.9-goolf-1.7.20.eb b/easybuild/easyconfigs/x/x265-1.9-goolf-1.7.20.eb new file mode 100644 index 0000000000..8c4df77f6d --- /dev/null +++ b/easybuild/easyconfigs/x/x265-1.9-goolf-1.7.20.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '1.9' + +homepage = 'http://www.videolan.org/developers/x265.html' +description = """x265 is a free software library and application for encoding video streams into the H.265 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + + +source_urls = ['http://ftp.videolan.org/pub/videolan/x265/'] +sources = ['x265_%(version)s.tar.gz'] + +dependencies = [('CMake', '2.8.11'), + ('Yasm','1.3.0'),] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 049151f640c7228f3c86b817be2d192a6325888a Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Fri, 20 May 2016 15:27:57 -0400 Subject: [PATCH 005/350] Create Yasm-1.3.0-goolf-1.7.20.eb you place the Yasm-1.3.0.tar.gz here $EASYBUILD_PREFIX/software/EasyBuild/2.6.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.6.0-py2.7.egg/easybuild/easyconfigs/y/Yasm/y/Yasm$ --- .../y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..250d77f32c --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' +#versionsuffix = '-20141219' + +description = "Yasm-1.3.0: Complete rewrite of the NASM assembler with BSD license" + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +homepage = 'http://www.tortall.net/projects/yasm/' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': [], ## fixme + 'dirs': ['.'], ## fixme +} + +parallel = 1 # this is a very conservative choice ## fixme +moduleclass = 'base' # please change this from base to right category ## fixme -- GitLab From ac4b898a536211cc8be7b3923dab5c6bad527149 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 May 2016 18:41:09 +0200 Subject: [PATCH 006/350] fix location of x265 easyconfig + minor style fixes --- .../easyconfigs/x/{ => x265}/x265-1.9-goolf-1.7.20.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/x/{ => x265}/x265-1.9-goolf-1.7.20.eb (88%) diff --git a/easybuild/easyconfigs/x/x265-1.9-goolf-1.7.20.eb b/easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb similarity index 88% rename from easybuild/easyconfigs/x/x265-1.9-goolf-1.7.20.eb rename to easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb index 8c4df77f6d..44548e3d8d 100644 --- a/easybuild/easyconfigs/x/x265-1.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb @@ -9,12 +9,13 @@ description = """x265 is a free software library and application for encoding vi toolchain = {'name': 'goolf', 'version': '1.7.20'} - source_urls = ['http://ftp.videolan.org/pub/videolan/x265/'] sources = ['x265_%(version)s.tar.gz'] -dependencies = [('CMake', '2.8.11'), - ('Yasm','1.3.0'),] +builddependencies = [('CMake', '2.8.11')] +dependencies = [ + ('Yasm','1.3.0'), +] start_dir = 'source' -- GitLab From f788f6e4f9ffce5eb1ec14e895c572788dfc8b2d Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Sat, 4 Jun 2016 09:01:35 +0400 Subject: [PATCH 007/350] adding easyconfigs for anaconda and condacreate --- .../easyconfigs/a/Anaconda/anaconda-2.4.0.eb | 42 +++++++++++++++++++ .../c/CondaCreate/condacreate-1.0.eb | 37 ++++++++++++++++ .../c/CondaCreate/requirements.txt | 1 + 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb create mode 100644 easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb create mode 100644 easybuild/easyconfigs/c/CondaCreate/requirements.txt diff --git a/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb new file mode 100644 index 0000000000..bd6762a52c --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb @@ -0,0 +1,42 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Authors:: Jillian Rowe +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_anaconda' + +name = "anaconda" +version = "2-4.0.0" +variant = "Linux-x86_64" + +homepage = "https://www.continuum.io/" +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +anaconda_version = 2 + +source_urls = ["http://repo.continuum.io/archive/Anaconda%s-%s.sh" % (version, variant)] +sources = ["Anaconda%s-%s.sh" % (version, variant)] +checksums = [ '31ed3ef07435d7068e1e03be49381b13' ] + +license_file = 'LICENSE.txt' + +sanity_check_paths = { + 'files': ["bin/pydoc"], + 'dirs': [] +} + +modextravars = { + 'ANACONDA_LICENSE': license_file, +} + +moduleclass = 'lang' +##Trailing comment diff --git a/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb b/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb new file mode 100644 index 0000000000..be9caec900 --- /dev/null +++ b/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb @@ -0,0 +1,37 @@ +## +# 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_CondaCreate' + +name = "condacreate-env" +version = "1.0" +variant = "Linux-x86_64" + +homepage = "https://github.com/bioconda/bioconda-recipes" +description = """ Conda is a platform- and language-independent package manager that sports easy distribution, installation and version management of software. The bioconda channel is a Conda channel providing bioinformatics related packages. This repository hosts the corresponding recipes. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['requirements.txt'] + +requirements = sources[0] +channels = 'bioconda' + +builddependencies = [('anaconda', '2-4.0.0')] + +sanity_check_paths = { + 'files': ["bin/cpanm"], + 'dirs': [] +} + +moduleclass = 'tools' +##Trailing comment diff --git a/easybuild/easyconfigs/c/CondaCreate/requirements.txt b/easybuild/easyconfigs/c/CondaCreate/requirements.txt new file mode 100644 index 0000000000..3806bb01ca --- /dev/null +++ b/easybuild/easyconfigs/c/CondaCreate/requirements.txt @@ -0,0 +1 @@ +perl-app-cpanminus -- GitLab From 3a4c789f1c99bfee23360b53858db72ea9f1db62 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Sat, 4 Jun 2016 09:01:35 +0400 Subject: [PATCH 008/350] adding easyconfigs for anaconda and condacreate --- .../easyconfigs/a/Anaconda/anaconda-2.4.0.eb | 42 +++++++++++++++++++ .../c/CondaCreate/condacreate-1.0.eb | 37 ++++++++++++++++ .../c/CondaCreate/requirements.txt | 1 + 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb create mode 100644 easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb create mode 100644 easybuild/easyconfigs/c/CondaCreate/requirements.txt diff --git a/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb new file mode 100644 index 0000000000..bd6762a52c --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb @@ -0,0 +1,42 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Authors:: Jillian Rowe +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_anaconda' + +name = "anaconda" +version = "2-4.0.0" +variant = "Linux-x86_64" + +homepage = "https://www.continuum.io/" +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +anaconda_version = 2 + +source_urls = ["http://repo.continuum.io/archive/Anaconda%s-%s.sh" % (version, variant)] +sources = ["Anaconda%s-%s.sh" % (version, variant)] +checksums = [ '31ed3ef07435d7068e1e03be49381b13' ] + +license_file = 'LICENSE.txt' + +sanity_check_paths = { + 'files': ["bin/pydoc"], + 'dirs': [] +} + +modextravars = { + 'ANACONDA_LICENSE': license_file, +} + +moduleclass = 'lang' +##Trailing comment diff --git a/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb b/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb new file mode 100644 index 0000000000..be9caec900 --- /dev/null +++ b/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb @@ -0,0 +1,37 @@ +## +# 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_CondaCreate' + +name = "condacreate-env" +version = "1.0" +variant = "Linux-x86_64" + +homepage = "https://github.com/bioconda/bioconda-recipes" +description = """ Conda is a platform- and language-independent package manager that sports easy distribution, installation and version management of software. The bioconda channel is a Conda channel providing bioinformatics related packages. This repository hosts the corresponding recipes. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['requirements.txt'] + +requirements = sources[0] +channels = 'bioconda' + +builddependencies = [('anaconda', '2-4.0.0')] + +sanity_check_paths = { + 'files': ["bin/cpanm"], + 'dirs': [] +} + +moduleclass = 'tools' +##Trailing comment diff --git a/easybuild/easyconfigs/c/CondaCreate/requirements.txt b/easybuild/easyconfigs/c/CondaCreate/requirements.txt new file mode 100644 index 0000000000..3806bb01ca --- /dev/null +++ b/easybuild/easyconfigs/c/CondaCreate/requirements.txt @@ -0,0 +1 @@ +perl-app-cpanminus -- GitLab From 707a5670567dd8e278a5719f1c5e41909e787164 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Wed, 13 Jul 2016 12:12:17 +0400 Subject: [PATCH 009/350] stupid case changes --- .../b/{BLASR => blasr (Case Conflict)}/BLASR-2.1-goolf-1.4.10.eb | 0 .../GraphViz-2.18-intel-2014b-Perl-5.20.0.eb | 0 .../g/{Grep => grep (Case Conflict)}/Grep-2.21-GCC-4.9.2.eb | 0 .../{GSL => gsl (Case Conflict)}/GSL-1.15-goalf-1.1.0-no-OFED.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.15-goolf-1.4.10.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.15-goolf-1.5.14.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.15-ictce-4.0.6.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.15-ictce-5.3.0.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.15-intel-2014b.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.15-intel-2015a.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-foss-2015a.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-foss-2015b.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-foss-2016a.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolf-1.4.10.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolf-1.5.14.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolf-1.7.20.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolfc-1.3.12.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolfc-2.6.10.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-ictce-5.3.0.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-ictce-5.4.0.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-ictce-5.5.0.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-ictce-6.2.5.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-intel-2014b.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-intel-2015a.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-intel-2015b.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-1.16-intel-2016a.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-2.1-foss-2015b.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-2.1-foss-2016a.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-2.1-intel-2015b.eb | 0 .../g/{GSL => gsl (Case Conflict)}/GSL-2.1-intel-2016a.eb | 0 .../Mawk-1.3.4-goolf-1.4.10-20150503.eb | 0 31 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/{BLASR => blasr (Case Conflict)}/BLASR-2.1-goolf-1.4.10.eb (100%) rename easybuild/easyconfigs/g/{GraphViz => Graphviz (Case Conflict)}/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb (100%) rename easybuild/easyconfigs/g/{Grep => grep (Case Conflict)}/Grep-2.21-GCC-4.9.2.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.15-goalf-1.1.0-no-OFED.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.15-goolf-1.4.10.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.15-goolf-1.5.14.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.15-ictce-4.0.6.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.15-ictce-5.3.0.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.15-intel-2014b.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.15-intel-2015a.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-foss-2015a.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-foss-2015b.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-foss-2016a.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolf-1.4.10.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolf-1.5.14.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolf-1.7.20.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolfc-1.3.12.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-goolfc-2.6.10.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-ictce-5.3.0.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-ictce-5.4.0.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-ictce-5.5.0.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-ictce-6.2.5.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-intel-2014b.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-intel-2015a.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-intel-2015b.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-1.16-intel-2016a.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-2.1-foss-2015b.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-2.1-foss-2016a.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-2.1-intel-2015b.eb (100%) rename easybuild/easyconfigs/g/{GSL => gsl (Case Conflict)}/GSL-2.1-intel-2016a.eb (100%) rename easybuild/easyconfigs/m/{Mawk => mawk (Case Conflict)}/Mawk-1.3.4-goolf-1.4.10-20150503.eb (100%) diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb similarity index 100% rename from easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb rename to easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb diff --git a/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb b/easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2.eb similarity index 100% rename from easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb rename to easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/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/g/gsl (Case Conflict)/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/g/gsl (Case Conflict)/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/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb similarity index 100% rename from easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb rename to easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb -- GitLab From c9fa017ce4128eafa60ff02b75b23675e9f7f95d Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Wed, 13 Jul 2016 12:13:18 +0400 Subject: [PATCH 010/350] what happens if i get rid of gsl --- .../GSL-1.15-goalf-1.1.0-no-OFED.eb | 19 ------------ .../GSL-1.15-goolf-1.4.10.eb | 19 ------------ .../GSL-1.15-goolf-1.5.14.eb | 19 ------------ .../GSL-1.15-ictce-4.0.6.eb | 19 ------------ .../GSL-1.15-ictce-5.3.0.eb | 19 ------------ .../GSL-1.15-intel-2014b.eb | 19 ------------ .../GSL-1.15-intel-2015a.eb | 19 ------------ .../GSL-1.16-foss-2015a.eb | 19 ------------ .../GSL-1.16-foss-2015b.eb | 19 ------------ .../GSL-1.16-foss-2016a.eb | 19 ------------ .../GSL-1.16-goolf-1.4.10.eb | 19 ------------ .../GSL-1.16-goolf-1.5.14.eb | 19 ------------ .../GSL-1.16-goolf-1.7.20.eb | 19 ------------ .../GSL-1.16-goolfc-1.3.12.eb | 19 ------------ .../GSL-1.16-goolfc-2.6.10.eb | 19 ------------ .../GSL-1.16-ictce-5.3.0.eb | 19 ------------ .../GSL-1.16-ictce-5.4.0.eb | 19 ------------ .../GSL-1.16-ictce-5.5.0.eb | 19 ------------ .../GSL-1.16-ictce-6.2.5.eb | 19 ------------ .../GSL-1.16-intel-2014b.eb | 19 ------------ .../GSL-1.16-intel-2015a.eb | 19 ------------ .../GSL-1.16-intel-2015b.eb | 19 ------------ .../GSL-1.16-intel-2016a.eb | 19 ------------ .../gsl (Case Conflict)/GSL-2.1-foss-2015b.eb | 19 ------------ .../gsl (Case Conflict)/GSL-2.1-foss-2016a.eb | 19 ------------ .../GSL-2.1-intel-2015b.eb | 19 ------------ .../GSL-2.1-intel-2016a.eb | 19 ------------ .../g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb | 29 ------------------- 28 files changed, 542 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb delete mode 100644 easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb deleted file mode 100644 index f4197820e5..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'goalf', 'version': '1.1.0-no-OFED'} -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/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb deleted file mode 100644 index d9295adc89..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'goolf', 'version': '1.4.10'} -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/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb deleted file mode 100644 index 3230d895d1..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'goolf', 'version': '1.5.14'} -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/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb deleted file mode 100644 index 93b875b8e7..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'ictce', 'version': '4.0.6'} -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/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb deleted file mode 100644 index 3e17c8b5d6..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'ictce', 'version': '5.3.0'} -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/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb deleted file mode 100644 index 9ef4e74b99..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': '2014b'} -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/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb deleted file mode 100644 index 2c856c0c22..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': '2015a'} -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/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb deleted file mode 100644 index 426a5fa702..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'foss', 'version': '2015a'} -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/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb deleted file mode 100644 index 681aa2648b..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'foss', 'version': '2015b'} -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/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb deleted file mode 100644 index 2cce073a65..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'foss', 'version': '2016a'} -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/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb deleted file mode 100644 index 7481f95582..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolf', 'version': '1.4.10'} -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/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb deleted file mode 100644 index 493418d259..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolf', 'version': '1.5.14'} -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/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb deleted file mode 100644 index 723ea8a309..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolf', 'version': '1.7.20'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = ['http://ftpmirror.gnu.org/gsl/'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb deleted file mode 100644 index 0336ef456f..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolfc', 'version': '1.3.12'} -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/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb deleted file mode 100644 index 0e558d5644..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolfc', 'version': '2.6.10'} -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/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb deleted file mode 100644 index e3cf37d1e5..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'ictce', 'version': '5.3.0'} -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/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb deleted file mode 100644 index 1ee8967b14..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'ictce', 'version': '5.4.0'} -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/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb deleted file mode 100644 index cc561c1cbf..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'ictce', 'version': '5.5.0'} -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/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb deleted file mode 100644 index e1a049a993..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'ictce', 'version': '6.2.5'} -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/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb deleted file mode 100644 index f93fbb1090..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': '2014b'} -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/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb deleted file mode 100644 index 207992d0eb..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': '2015a'} -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/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb deleted file mode 100644 index 33c068c25d..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': '2015b'} -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/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb deleted file mode 100644 index aaffd974f5..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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 = {'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/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb deleted file mode 100644 index 64966f0023..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb +++ /dev/null @@ -1,19 +0,0 @@ -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 = {'version': '2015b', 'name': 'foss'} -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/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb deleted file mode 100644 index f4a28c0d8f..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb +++ /dev/null @@ -1,19 +0,0 @@ -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 = {'version': '2016a', 'name': 'foss'} -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/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb deleted file mode 100644 index d363055a95..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb +++ /dev/null @@ -1,19 +0,0 @@ -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': '2015b'} -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/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb deleted file mode 100644 index 6ff19555c3..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb +++ /dev/null @@ -1,19 +0,0 @@ -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': '2016a'} -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/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb deleted file mode 100644 index 36d3ba6863..0000000000 --- a/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'RPackage' - -name = 'gsl' -version = '1.9-10' - -homepage = 'http://cran.r-project.org/web/packages/gsl' -description = """An R wrapper for the special functions and quasi random number generators of the Gnu Scientific - Library (GSL).""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://cran.r-project.org/src/contrib/'] -sources = ['%(name)s_%(version)s.tar.gz'] - -r = 'R' -rver = '3.1.1' -versionsuffix = '-%s-%s' % (r, rver) - -dependencies = [ - (r, rver), - ('GSL', '1.16'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['gsl'], -} - -moduleclass = 'math' -- GitLab From 0386440ea542db9b0d1e95ee1765aca613df9a8d Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Wed, 13 Jul 2016 12:33:22 +0400 Subject: [PATCH 011/350] fixing my conflicts with blunt force trauma --- .../easyconfigs/a/Anaconda/anaconda-2.4.0.eb | 42 ------------------- .../BLASR-2.1-goolf-1.4.10.eb | 0 .../c/CondaCreate/condacreate-1.0.eb | 37 ---------------- .../c/CondaCreate/requirements.txt | 1 - .../g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb | 19 +++++++++ .../g/GSL/GSL-1.15-goolf-1.4.10.eb | 19 +++++++++ .../g/GSL/GSL-1.15-goolf-1.5.14.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb | 19 +++++++++ .../g/GSL/GSL-1.16-goolf-1.4.10.eb | 19 +++++++++ .../g/GSL/GSL-1.16-goolf-1.5.14.eb | 19 +++++++++ .../g/GSL/GSL-1.16-goolf-1.7.20.eb | 19 +++++++++ .../g/GSL/GSL-1.16-goolfc-1.3.12.eb | 19 +++++++++ .../g/GSL/GSL-1.16-goolfc-2.6.10.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb | 19 +++++++++ .../easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb | 19 +++++++++ .../GraphViz-2.18-intel-2014b-Perl-5.20.0.eb | 0 .../Grep-2.21-GCC-4.9.2.eb | 0 .../g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb | 29 +++++++++++++ .../Mawk-1.3.4-goolf-1.4.10-20150503.eb | 0 35 files changed, 542 insertions(+), 80 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb rename easybuild/easyconfigs/b/{blasr (Case Conflict) => BLASR}/BLASR-2.1-goolf-1.4.10.eb (100%) delete mode 100644 easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb delete mode 100644 easybuild/easyconfigs/c/CondaCreate/requirements.txt create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb rename easybuild/easyconfigs/g/{Graphviz (Case Conflict) => GraphViz}/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb (100%) rename easybuild/easyconfigs/g/{grep (Case Conflict) => Grep}/Grep-2.21-GCC-4.9.2.eb (100%) create mode 100644 easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb rename easybuild/easyconfigs/m/{mawk (Case Conflict) => Mawk}/Mawk-1.3.4-goolf-1.4.10-20150503.eb (100%) diff --git a/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb deleted file mode 100644 index bd6762a52c..0000000000 --- a/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# -# Authors:: Jillian Rowe -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_anaconda' - -name = "anaconda" -version = "2-4.0.0" -variant = "Linux-x86_64" - -homepage = "https://www.continuum.io/" -description = """Built to complement the rich, open source Python community, -the Anaconda platform provides an enterprise-ready data analytics platform -that empowers companies to adopt a modern open data science analytics architecture. -""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -anaconda_version = 2 - -source_urls = ["http://repo.continuum.io/archive/Anaconda%s-%s.sh" % (version, variant)] -sources = ["Anaconda%s-%s.sh" % (version, variant)] -checksums = [ '31ed3ef07435d7068e1e03be49381b13' ] - -license_file = 'LICENSE.txt' - -sanity_check_paths = { - 'files': ["bin/pydoc"], - 'dirs': [] -} - -modextravars = { - 'ANACONDA_LICENSE': license_file, -} - -moduleclass = 'lang' -##Trailing comment diff --git a/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb b/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb deleted file mode 100644 index be9caec900..0000000000 --- a/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# 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_CondaCreate' - -name = "condacreate-env" -version = "1.0" -variant = "Linux-x86_64" - -homepage = "https://github.com/bioconda/bioconda-recipes" -description = """ Conda is a platform- and language-independent package manager that sports easy distribution, installation and version management of software. The bioconda channel is a Conda channel providing bioinformatics related packages. This repository hosts the corresponding recipes. """ - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['requirements.txt'] - -requirements = sources[0] -channels = 'bioconda' - -builddependencies = [('anaconda', '2-4.0.0')] - -sanity_check_paths = { - 'files': ["bin/cpanm"], - 'dirs': [] -} - -moduleclass = 'tools' -##Trailing comment diff --git a/easybuild/easyconfigs/c/CondaCreate/requirements.txt b/easybuild/easyconfigs/c/CondaCreate/requirements.txt deleted file mode 100644 index 3806bb01ca..0000000000 --- a/easybuild/easyconfigs/c/CondaCreate/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -perl-app-cpanminus diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..f4197820e5 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'goalf', 'version': '1.1.0-no-OFED'} +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/GSL/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb new file mode 100644 index 0000000000..d9295adc89 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'goolf', 'version': '1.4.10'} +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/GSL/GSL-1.15-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb new file mode 100644 index 0000000000..3230d895d1 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'goolf', 'version': '1.5.14'} +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/GSL/GSL-1.15-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb new file mode 100644 index 0000000000..93b875b8e7 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'ictce', 'version': '4.0.6'} +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/GSL/GSL-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb new file mode 100644 index 0000000000..3e17c8b5d6 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'ictce', 'version': '5.3.0'} +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/GSL/GSL-1.15-intel-2014b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb new file mode 100644 index 0000000000..9ef4e74b99 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': '2014b'} +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/GSL/GSL-1.15-intel-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb new file mode 100644 index 0000000000..2c856c0c22 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': '2015a'} +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/GSL/GSL-1.16-foss-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb new file mode 100644 index 0000000000..426a5fa702 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'foss', 'version': '2015a'} +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/GSL/GSL-1.16-foss-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb new file mode 100644 index 0000000000..681aa2648b --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'foss', 'version': '2015b'} +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/GSL/GSL-1.16-foss-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb new file mode 100644 index 0000000000..2cce073a65 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'foss', 'version': '2016a'} +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/GSL/GSL-1.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb new file mode 100644 index 0000000000..7481f95582 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolf', 'version': '1.4.10'} +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/GSL/GSL-1.16-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb new file mode 100644 index 0000000000..493418d259 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolf', 'version': '1.5.14'} +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/GSL/GSL-1.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb new file mode 100644 index 0000000000..723ea8a309 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://ftpmirror.gnu.org/gsl/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb new file mode 100644 index 0000000000..0336ef456f --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolfc', 'version': '1.3.12'} +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/GSL/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb new file mode 100644 index 0000000000..0e558d5644 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolfc', 'version': '2.6.10'} +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/GSL/GSL-1.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb new file mode 100644 index 0000000000..e3cf37d1e5 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'ictce', 'version': '5.3.0'} +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/GSL/GSL-1.16-ictce-5.4.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb new file mode 100644 index 0000000000..1ee8967b14 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'ictce', 'version': '5.4.0'} +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/GSL/GSL-1.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb new file mode 100644 index 0000000000..cc561c1cbf --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'ictce', 'version': '5.5.0'} +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/GSL/GSL-1.16-ictce-6.2.5.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb new file mode 100644 index 0000000000..e1a049a993 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'ictce', 'version': '6.2.5'} +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/GSL/GSL-1.16-intel-2014b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb new file mode 100644 index 0000000000..f93fbb1090 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': '2014b'} +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/GSL/GSL-1.16-intel-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb new file mode 100644 index 0000000000..207992d0eb --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': '2015a'} +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/GSL/GSL-1.16-intel-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb new file mode 100644 index 0000000000..33c068c25d --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': '2015b'} +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/GSL/GSL-1.16-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb new file mode 100644 index 0000000000..aaffd974f5 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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 = {'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/GSL/GSL-2.1-foss-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb new file mode 100644 index 0000000000..64966f0023 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.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 = {'version': '2015b', 'name': 'foss'} +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/GSL/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb new file mode 100644 index 0000000000..f4a28c0d8f --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.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 = {'version': '2016a', 'name': 'foss'} +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/GSL/GSL-2.1-intel-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb new file mode 100644 index 0000000000..d363055a95 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.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': '2015b'} +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/GSL/GSL-2.1-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb new file mode 100644 index 0000000000..6ff19555c3 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.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': '2016a'} +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/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb similarity index 100% rename from easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb rename to easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb diff --git a/easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2.eb b/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb similarity index 100% rename from easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2.eb rename to easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb new file mode 100644 index 0000000000..36d3ba6863 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'gsl' +version = '1.9-10' + +homepage = 'http://cran.r-project.org/web/packages/gsl' +description = """An R wrapper for the special functions and quasi random number generators of the Gnu Scientific + Library (GSL).""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cran.r-project.org/src/contrib/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.1.1' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('GSL', '1.16'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['gsl'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb similarity index 100% rename from easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb rename to easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb -- GitLab From ab44ab8c3c3edceb96506724b3b6d2180d2dd61e Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Wed, 13 Jul 2016 12:45:39 +0400 Subject: [PATCH 012/350] commiting --- .../GraphViz-2.18-intel-2014b-Perl-5.20.0.eb | 0 .../g/{Grep => grep (Case Conflict)}/Grep-2.21-GCC-4.9.2.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{GraphViz => Graphviz (Case Conflict)}/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb (100%) rename easybuild/easyconfigs/g/{Grep => grep (Case Conflict)}/Grep-2.21-GCC-4.9.2.eb (100%) diff --git a/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb similarity index 100% rename from easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb rename to easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb diff --git a/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb b/easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2.eb similarity index 100% rename from easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb rename to easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2.eb -- GitLab From 55cf477231502ee522fe4263d42a01bab0a508ff Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Wed, 13 Jul 2016 12:47:00 +0400 Subject: [PATCH 013/350] commiting --- .../BLASR-2.1-goolf-1.4.10 (1).eb} | 0 .../BLASR-2.1-goolf-1.4.10.eb | 37 +++++++++++++++++++ .../GraphViz-2.18-intel-2014b-Perl-5.20.0.eb | 32 ++++++++++++++++ .../easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb | 19 ++++++++++ .../GSL-1.15-goalf-1.1.0-no-OFED.eb | 19 ++++++++++ .../GSL-1.15-goolf-1.4.10.eb | 19 ++++++++++ .../GSL-1.15-goolf-1.5.14.eb | 19 ++++++++++ .../GSL-1.15-ictce-4.0.6.eb | 19 ++++++++++ .../GSL-1.15-ictce-5.3.0.eb | 19 ++++++++++ .../GSL-1.15-intel-2014b.eb | 19 ++++++++++ .../GSL-1.15-intel-2015a.eb | 19 ++++++++++ .../GSL-1.16-foss-2015a.eb | 19 ++++++++++ .../GSL-1.16-foss-2015b.eb | 19 ++++++++++ .../GSL-1.16-foss-2016a.eb | 19 ++++++++++ .../GSL-1.16-goolf-1.4.10.eb | 19 ++++++++++ .../GSL-1.16-goolf-1.5.14.eb | 19 ++++++++++ .../GSL-1.16-goolf-1.7.20.eb | 19 ++++++++++ .../GSL-1.16-goolfc-1.3.12.eb | 19 ++++++++++ .../GSL-1.16-goolfc-2.6.10.eb | 19 ++++++++++ .../GSL-1.16-ictce-5.3.0.eb | 19 ++++++++++ .../GSL-1.16-ictce-5.4.0.eb | 19 ++++++++++ .../GSL-1.16-ictce-5.5.0.eb | 19 ++++++++++ .../GSL-1.16-ictce-6.2.5.eb | 19 ++++++++++ .../GSL-1.16-intel-2014b.eb | 19 ++++++++++ .../GSL-1.16-intel-2015a.eb | 19 ++++++++++ .../GSL-1.16-intel-2015b.eb | 19 ++++++++++ .../GSL-1.16-intel-2016a.eb | 19 ++++++++++ .../gsl (Case Conflict)/GSL-2.1-foss-2015b.eb | 19 ++++++++++ .../gsl (Case Conflict)/GSL-2.1-foss-2016a.eb | 19 ++++++++++ .../GSL-2.1-intel-2015b.eb | 19 ++++++++++ .../GSL-2.1-intel-2016a.eb | 19 ++++++++++ .../Mawk-1.3.4-goolf-1.4.10-20150503 (1).eb} | 0 .../Mawk-1.3.4-goolf-1.4.10-20150503.eb | 27 ++++++++++++++ 33 files changed, 628 insertions(+) rename easybuild/easyconfigs/b/{BLASR/BLASR-2.1-goolf-1.4.10.eb => blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10 (1).eb} (100%) create mode 100644 easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb create mode 100644 easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb rename easybuild/easyconfigs/m/{Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb => mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503 (1).eb} (100%) create mode 100644 easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10 (1).eb similarity index 100% rename from easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10 (1).eb diff --git a/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..7b47764f47 --- /dev/null +++ b/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'BLASR' +version = '2.1' + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """ BLASR (Basic Local Alignment with Successive Refinement) rapidly maps + reads to genomes by finding the highest scoring local alignment or set of local alignments + between the read and the genome. Optimized for PacBio's extraordinarily long reads and + taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] +sources = ['smrtanalysis-%(version)s.tar.gz'] + +dependencies = [('HDF5', '1.8.11')] + +skipsteps = ['configure'] + +# the STATIC= option is a workaround. Check details here: +# https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 +buildopts = ' STATIC= ' + +installopts = ' INSTALL_BIN_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ["bin/blasr"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000..4dc6df7462 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'GraphViz' +version = '2.18' + +homepage = 'https://metacpan.org/pod/GraphViz' +description = """This module provides a Perl interface to the amazing Graphviz, +an open source graph visualization tool from AT&T.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'] +sources = [SOURCE_TGZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("Graphviz", "2.38.0"), +] + +options = {'modulename': 'GraphViz'} + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/GraphViz.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/GraphViz' % (perlmajver, perlver)], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb b/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb new file mode 100644 index 0000000000..43c5a459fa --- /dev/null +++ b/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'Grep' +version = '2.21' + +homepage = 'http://www.gnu.org/software/grep/' +description = """The grep command searches one or more input files for lines containing a match to a specified pattern. By default, grep prints the matching lines.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] + +sanity_check_paths = { + 'files': [], + 'dirs': ["bin"] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..f4197820e5 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'goalf', 'version': '1.1.0-no-OFED'} +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/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb new file mode 100644 index 0000000000..d9295adc89 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'goolf', 'version': '1.4.10'} +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/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb new file mode 100644 index 0000000000..3230d895d1 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'goolf', 'version': '1.5.14'} +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/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb new file mode 100644 index 0000000000..93b875b8e7 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'ictce', 'version': '4.0.6'} +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/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb new file mode 100644 index 0000000000..3e17c8b5d6 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': 'ictce', 'version': '5.3.0'} +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/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb new file mode 100644 index 0000000000..9ef4e74b99 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': '2014b'} +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/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb new file mode 100644 index 0000000000..2c856c0c22 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +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': '2015a'} +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/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb new file mode 100644 index 0000000000..426a5fa702 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'foss', 'version': '2015a'} +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/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb new file mode 100644 index 0000000000..681aa2648b --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'foss', 'version': '2015b'} +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/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb new file mode 100644 index 0000000000..2cce073a65 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'foss', 'version': '2016a'} +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/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb new file mode 100644 index 0000000000..7481f95582 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolf', 'version': '1.4.10'} +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/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb new file mode 100644 index 0000000000..493418d259 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolf', 'version': '1.5.14'} +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/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb new file mode 100644 index 0000000000..723ea8a309 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://ftpmirror.gnu.org/gsl/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb new file mode 100644 index 0000000000..0336ef456f --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolfc', 'version': '1.3.12'} +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/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb new file mode 100644 index 0000000000..0e558d5644 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'goolfc', 'version': '2.6.10'} +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/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb new file mode 100644 index 0000000000..e3cf37d1e5 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'ictce', 'version': '5.3.0'} +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/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb new file mode 100644 index 0000000000..1ee8967b14 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'ictce', 'version': '5.4.0'} +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/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb new file mode 100644 index 0000000000..cc561c1cbf --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'ictce', 'version': '5.5.0'} +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/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb new file mode 100644 index 0000000000..e1a049a993 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': 'ictce', 'version': '6.2.5'} +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/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb new file mode 100644 index 0000000000..f93fbb1090 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': '2014b'} +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/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb new file mode 100644 index 0000000000..207992d0eb --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': '2015a'} +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/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb new file mode 100644 index 0000000000..33c068c25d --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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': '2015b'} +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/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb new file mode 100644 index 0000000000..aaffd974f5 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +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 = {'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/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb new file mode 100644 index 0000000000..64966f0023 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.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 = {'version': '2015b', 'name': 'foss'} +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/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb new file mode 100644 index 0000000000..f4a28c0d8f --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.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 = {'version': '2016a', 'name': 'foss'} +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/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb new file mode 100644 index 0000000000..d363055a95 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.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': '2015b'} +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/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb new file mode 100644 index 0000000000..6ff19555c3 --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.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': '2016a'} +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/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503 (1).eb similarity index 100% rename from easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb rename to easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503 (1).eb diff --git a/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb new file mode 100644 index 0000000000..7235621e5d --- /dev/null +++ b/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb @@ -0,0 +1,27 @@ +# 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 = 'Mawk' +version = '1.3.4' +versionsuffix = '-20150503' + +homepage = 'http://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['ftp://invisible-island.net/mawk/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 371c7c1f2963580e5d1db78288c86ce2cb3860bb Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Wed, 13 Jul 2016 12:54:04 +0400 Subject: [PATCH 014/350] fix master and then develop --- ...phViz-2.18-intel-2014b-Perl-5.20.0 (1).eb} | 0 .../Grep-2.21-GCC-4.9.2 (1).eb} | 0 .../GSL-1.15-goalf-1.1.0-no-OFED (1).eb} | 0 .../GSL-1.15-goolf-1.4.10 (1).eb} | 0 .../GSL-1.15-goolf-1.5.14 (1).eb} | 0 .../GSL-1.15-ictce-4.0.6 (1).eb} | 0 .../GSL-1.15-ictce-5.3.0 (1).eb} | 0 .../GSL-1.15-intel-2014b (1).eb} | 0 .../GSL-1.15-intel-2015a (1).eb} | 0 .../GSL-1.16-foss-2015a (1).eb} | 0 .../GSL-1.16-foss-2015b (1).eb} | 0 .../GSL-1.16-foss-2016a (1).eb} | 0 .../GSL-1.16-goolf-1.4.10 (1).eb} | 0 .../GSL-1.16-goolf-1.5.14 (1).eb} | 0 .../GSL-1.16-goolf-1.7.20 (1).eb} | 0 .../GSL-1.16-goolfc-1.3.12 (1).eb} | 0 .../GSL-1.16-goolfc-2.6.10 (1).eb} | 0 .../GSL-1.16-ictce-5.3.0 (1).eb} | 0 .../GSL-1.16-ictce-5.4.0 (1).eb} | 0 .../GSL-1.16-ictce-5.5.0 (1).eb} | 0 .../GSL-1.16-ictce-6.2.5 (1).eb} | 0 .../GSL-1.16-intel-2014b (1).eb} | 0 .../GSL-1.16-intel-2015a (1).eb} | 0 .../GSL-1.16-intel-2015b (1).eb} | 0 .../GSL-1.16-intel-2016a (1).eb} | 0 .../GSL-2.1-CrayGNU-2015.11.eb | 24 +++++++++++++++ .../GSL-2.1-foss-2015b (1).eb} | 0 .../GSL-2.1-foss-2016a (1).eb} | 0 .../GSL-2.1-intel-2015b (1).eb} | 0 .../GSL-2.1-intel-2016a (1).eb} | 0 .../Guile-2.0.11-foss-2016a.eb | 30 +++++++++++++++++++ 31 files changed, 54 insertions(+) rename easybuild/easyconfigs/g/{GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb => Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0 (1).eb} (100%) rename easybuild/easyconfigs/g/{Grep/Grep-2.21-GCC-4.9.2.eb => grep (Case Conflict)/Grep-2.21-GCC-4.9.2 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb => gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.15-goolf-1.4.10.eb => gsl (Case Conflict)/GSL-1.15-goolf-1.4.10 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.15-goolf-1.5.14.eb => gsl (Case Conflict)/GSL-1.15-goolf-1.5.14 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.15-ictce-4.0.6.eb => gsl (Case Conflict)/GSL-1.15-ictce-4.0.6 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.15-ictce-5.3.0.eb => gsl (Case Conflict)/GSL-1.15-ictce-5.3.0 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.15-intel-2014b.eb => gsl (Case Conflict)/GSL-1.15-intel-2014b (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.15-intel-2015a.eb => gsl (Case Conflict)/GSL-1.15-intel-2015a (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-foss-2015a.eb => gsl (Case Conflict)/GSL-1.16-foss-2015a (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-foss-2015b.eb => gsl (Case Conflict)/GSL-1.16-foss-2015b (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-foss-2016a.eb => gsl (Case Conflict)/GSL-1.16-foss-2016a (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-goolf-1.4.10.eb => gsl (Case Conflict)/GSL-1.16-goolf-1.4.10 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-goolf-1.5.14.eb => gsl (Case Conflict)/GSL-1.16-goolf-1.5.14 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-goolf-1.7.20.eb => gsl (Case Conflict)/GSL-1.16-goolf-1.7.20 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-goolfc-1.3.12.eb => gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-goolfc-2.6.10.eb => gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-ictce-5.3.0.eb => gsl (Case Conflict)/GSL-1.16-ictce-5.3.0 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-ictce-5.4.0.eb => gsl (Case Conflict)/GSL-1.16-ictce-5.4.0 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-ictce-5.5.0.eb => gsl (Case Conflict)/GSL-1.16-ictce-5.5.0 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-ictce-6.2.5.eb => gsl (Case Conflict)/GSL-1.16-ictce-6.2.5 (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-intel-2014b.eb => gsl (Case Conflict)/GSL-1.16-intel-2014b (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-intel-2015a.eb => gsl (Case Conflict)/GSL-1.16-intel-2015a (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-intel-2015b.eb => gsl (Case Conflict)/GSL-1.16-intel-2015b (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-1.16-intel-2016a.eb => gsl (Case Conflict)/GSL-1.16-intel-2016a (1).eb} (100%) create mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-CrayGNU-2015.11.eb rename easybuild/easyconfigs/g/{GSL/GSL-2.1-foss-2015b.eb => gsl (Case Conflict)/GSL-2.1-foss-2015b (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-2.1-foss-2016a.eb => gsl (Case Conflict)/GSL-2.1-foss-2016a (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-2.1-intel-2015b.eb => gsl (Case Conflict)/GSL-2.1-intel-2015b (1).eb} (100%) rename easybuild/easyconfigs/g/{GSL/GSL-2.1-intel-2016a.eb => gsl (Case Conflict)/GSL-2.1-intel-2016a (1).eb} (100%) create mode 100644 easybuild/easyconfigs/g/guile (Case Conflict)/Guile-2.0.11-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb rename to easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0 (1).eb diff --git a/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb b/easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb rename to easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2014b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2016a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.5.14.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5 (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5 (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a (1).eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000..378ea5f63e --- /dev/null +++ b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-CrayGNU-2015.11.eb @@ -0,0 +1,24 @@ +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': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths={ + 'files': ['lib/libgsl.so', 'lib/libgsl.a'], + 'dirs': ['include'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b (1).eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a (1).eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb rename to easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a (1).eb diff --git a/easybuild/easyconfigs/g/guile (Case Conflict)/Guile-2.0.11-foss-2016a.eb b/easybuild/easyconfigs/g/guile (Case Conflict)/Guile-2.0.11-foss-2016a.eb new file mode 100644 index 0000000000..94a0abd7af --- /dev/null +++ b/easybuild/easyconfigs/g/guile (Case Conflict)/Guile-2.0.11-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.0.11' + +homepage = 'https://www.gnu.org/software/guile/' +description = """Guile is a programming language, designed to help programmers create flexible applications that + can be extended by users or other programmers with plug-ins, modules, or scripts.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] +dependencies = [ + ('libunistring', '0.9.3'), + ('libffi', '3.2.1'), + ('gc', '7.4.4'), + ('GMP', '6.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' -- GitLab From 3f0e33a5010934ced203e7ccb9e316fa02165218 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Wed, 13 Jul 2016 12:55:52 +0400 Subject: [PATCH 015/350] commiting --- .../BLASR-2.1-goolf-1.4.10.eb | 0 .../BLASR-2.1-goolf-1.4.10 (1).eb | 37 ------------------- .../GSL-1.15-goalf-1.1.0-no-OFED.eb | 0 .../GSL-1.15-goolf-1.4.10.eb | 0 .../GSL-1.15-goolf-1.5.14.eb | 0 .../GSL-1.15-ictce-4.0.6.eb | 0 .../GSL-1.15-ictce-5.3.0.eb | 0 .../GSL-1.15-intel-2014b.eb | 0 .../GSL-1.15-intel-2015a.eb | 0 .../GSL-1.16-foss-2015a.eb | 0 .../GSL-1.16-foss-2015b.eb | 0 .../GSL-1.16-foss-2016a.eb | 0 .../GSL-1.16-goolf-1.4.10.eb | 0 .../GSL-1.16-goolf-1.5.14.eb | 0 .../GSL-1.16-goolf-1.7.20.eb | 0 .../GSL-1.16-goolfc-1.3.12.eb | 0 .../GSL-1.16-goolfc-2.6.10.eb | 0 .../GSL-1.16-ictce-5.3.0.eb | 0 .../GSL-1.16-ictce-5.4.0.eb | 0 .../GSL-1.16-ictce-5.5.0.eb | 0 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19 ---------- .../GSL-1.16-goolf-1.5.14 (1).eb | 19 ---------- .../GSL-1.16-goolf-1.7.20 (1).eb | 19 ---------- .../GSL-1.16-goolfc-1.3.12 (1).eb | 19 ---------- .../GSL-1.16-goolfc-2.6.10 (1).eb | 19 ---------- .../GSL-1.16-ictce-5.3.0 (1).eb | 19 ---------- .../GSL-1.16-ictce-5.4.0 (1).eb | 19 ---------- .../GSL-1.16-ictce-5.5.0 (1).eb | 19 ---------- .../GSL-1.16-ictce-6.2.5 (1).eb | 19 ---------- .../GSL-1.16-intel-2014b (1).eb | 19 ---------- .../GSL-1.16-intel-2015a (1).eb | 19 ---------- .../GSL-1.16-intel-2015b (1).eb | 19 ---------- .../GSL-1.16-intel-2016a (1).eb | 19 ---------- .../GSL-2.1-CrayGNU-2015.11.eb | 24 ------------ .../GSL-2.1-foss-2015b (1).eb | 19 ---------- .../GSL-2.1-foss-2016a (1).eb | 19 ---------- .../GSL-2.1-intel-2015b (1).eb | 19 ---------- .../GSL-2.1-intel-2016a (1).eb | 19 ---------- .../Guile-2.0.11-foss-2016a.eb | 30 --------------- .../Mawk-1.3.4-goolf-1.4.10-20150503.eb | 0 .../Mawk-1.3.4-goolf-1.4.10-20150503 (1).eb | 27 -------------- 64 files changed, 682 deletions(-) rename easybuild/easyconfigs/b/{blasr (Case Conflict) => BLASR}/BLASR-2.1-goolf-1.4.10.eb (100%) delete mode 100644 easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10 (1).eb rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.15-goalf-1.1.0-no-OFED.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.15-goolf-1.4.10.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.15-goolf-1.5.14.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.15-ictce-4.0.6.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.15-ictce-5.3.0.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.15-intel-2014b.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.15-intel-2015a.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-foss-2015a.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-foss-2015b.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-foss-2016a.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-goolf-1.4.10.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-goolf-1.5.14.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-goolf-1.7.20.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-goolfc-1.3.12.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-goolfc-2.6.10.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-ictce-5.3.0.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-ictce-5.4.0.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-ictce-5.5.0.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-ictce-6.2.5.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-intel-2014b.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-intel-2015a.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-intel-2015b.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-1.16-intel-2016a.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-2.1-foss-2015b.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-2.1-foss-2016a.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-2.1-intel-2015b.eb (100%) rename easybuild/easyconfigs/g/{gsl (Case Conflict) => GSL}/GSL-2.1-intel-2016a.eb (100%) rename easybuild/easyconfigs/g/{Graphviz (Case Conflict) => GraphViz}/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb (100%) delete mode 100644 easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0 (1).eb rename easybuild/easyconfigs/g/{grep (Case Conflict) => Grep}/Grep-2.21-GCC-4.9.2.eb (100%) delete mode 100644 easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2 (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10 (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14 (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6 (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0 (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b (1).eb delete mode 100644 easybuild/easyconfigs/g/gsl 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(1).eb diff --git a/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10 (1).eb b/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10 (1).eb deleted file mode 100644 index 7b47764f47..0000000000 --- a/easybuild/easyconfigs/b/blasr (Case Conflict)/BLASR-2.1-goolf-1.4.10 (1).eb +++ /dev/null @@ -1,37 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel - -easyblock = 'ConfigureMake' - -name = 'BLASR' -version = '2.1' - -homepage = 'https://github.com/PacificBiosciences/blasr' -description = """ BLASR (Basic Local Alignment with Successive Refinement) rapidly maps - reads to genomes by finding the highest scoring local alignment or set of local alignments - between the read and the genome. Optimized for PacBio's extraordinarily long reads and - taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. """ - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] -sources = ['smrtanalysis-%(version)s.tar.gz'] - -dependencies = [('HDF5', '1.8.11')] - -skipsteps = ['configure'] - -# the STATIC= option is a workaround. Check details here: -# https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 -buildopts = ' STATIC= ' - -installopts = ' INSTALL_BIN_DIR=%(installdir)s/bin' - -sanity_check_paths = { - 'files': ["bin/blasr"], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14.eb 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Conflict)/GSL-1.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2014b.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2015b.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a.eb rename to easybuild/easyconfigs/g/GSL/GSL-1.16-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b.eb rename to easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2015b.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a.eb rename to easybuild/easyconfigs/g/GSL/GSL-2.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b.eb rename to easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2015b.eb diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a.eb rename to easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016a.eb diff --git a/easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb similarity index 100% rename from easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb rename to easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb diff --git a/easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0 (1).eb b/easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0 (1).eb deleted file mode 100644 index 4dc6df7462..0000000000 --- a/easybuild/easyconfigs/g/Graphviz (Case Conflict)/GraphViz-2.18-intel-2014b-Perl-5.20.0 (1).eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PerlModule' - -name = 'GraphViz' -version = '2.18' - -homepage = 'https://metacpan.org/pod/GraphViz' -description = """This module provides a Perl interface to the amazing Graphviz, -an open source graph visualization tool from AT&T.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -source_urls = ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'] -sources = [SOURCE_TGZ] - -perl = 'Perl' -perlver = '5.20.0' -versionsuffix = '-%s-%s' % (perl, perlver) - -dependencies = [ - (perl, perlver), - ("Graphviz", "2.38.0"), -] - -options = {'modulename': 'GraphViz'} - -perlmajver = perlver.split('.')[0] -sanity_check_paths = { - 'files': ['lib/perl%s/site_perl/%s/GraphViz.pm' % (perlmajver, perlver)], - 'dirs': ['lib/perl%s/site_perl/%s/GraphViz' % (perlmajver, perlver)], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2.eb b/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb similarity index 100% rename from easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2.eb rename to easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2 (1).eb b/easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2 (1).eb deleted file mode 100644 index 43c5a459fa..0000000000 --- a/easybuild/easyconfigs/g/grep (Case Conflict)/Grep-2.21-GCC-4.9.2 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Grep' -version = '2.21' - -homepage = 'http://www.gnu.org/software/grep/' -description = """The grep command searches one or more input files for lines containing a match to a specified pattern. By default, grep prints the matching lines.""" - -toolchain = {'name': 'GCC', 'version': '4.9.2'} - -sources = [SOURCELOWER_TAR_XZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] - -sanity_check_paths = { - 'files': [], - 'dirs': ["bin"] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED (1).eb deleted file mode 100644 index f4197820e5..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goalf-1.1.0-no-OFED (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'goalf', 'version': '1.1.0-no-OFED'} -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/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10 (1).eb deleted file mode 100644 index d9295adc89..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.4.10 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'goolf', 'version': '1.4.10'} -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/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14 (1).eb deleted file mode 100644 index 3230d895d1..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-goolf-1.5.14 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'goolf', 'version': '1.5.14'} -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/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6 (1).eb deleted file mode 100644 index 93b875b8e7..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-4.0.6 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'ictce', 'version': '4.0.6'} -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/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0 (1).eb deleted file mode 100644 index 3e17c8b5d6..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-ictce-5.3.0 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': 'ictce', 'version': '5.3.0'} -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/gsl (Case Conflict)/GSL-1.15-intel-2014b (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b (1).eb deleted file mode 100644 index 9ef4e74b99..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2014b (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': '2014b'} -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/gsl (Case Conflict)/GSL-1.15-intel-2015a (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a (1).eb deleted file mode 100644 index 2c856c0c22..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.15-intel-2015a (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.15' - -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': '2015a'} -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/gsl (Case Conflict)/GSL-1.16-foss-2015a (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a (1).eb deleted file mode 100644 index 426a5fa702..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015a (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'foss', 'version': '2015a'} -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/gsl (Case Conflict)/GSL-1.16-foss-2015b (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b (1).eb deleted file mode 100644 index 681aa2648b..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2015b (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'foss', 'version': '2015b'} -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/gsl (Case Conflict)/GSL-1.16-foss-2016a (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a (1).eb deleted file mode 100644 index 2cce073a65..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-foss-2016a (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'foss', 'version': '2016a'} -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/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10 (1).eb deleted file mode 100644 index 7481f95582..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.4.10 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolf', 'version': '1.4.10'} -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/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14 (1).eb deleted file mode 100644 index 493418d259..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.5.14 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolf', 'version': '1.5.14'} -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/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20 (1).eb deleted file mode 100644 index 723ea8a309..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolf-1.7.20 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolf', 'version': '1.7.20'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = ['http://ftpmirror.gnu.org/gsl/'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12 (1).eb deleted file mode 100644 index 0336ef456f..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-1.3.12 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolfc', 'version': '1.3.12'} -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/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10 (1).eb deleted file mode 100644 index 0e558d5644..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-goolfc-2.6.10 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'goolfc', 'version': '2.6.10'} -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/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0 (1).eb deleted file mode 100644 index e3cf37d1e5..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.3.0 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'ictce', 'version': '5.3.0'} -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/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0 (1).eb deleted file mode 100644 index 1ee8967b14..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.4.0 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'ictce', 'version': '5.4.0'} -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/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0 (1).eb deleted file mode 100644 index cc561c1cbf..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-5.5.0 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'ictce', 'version': '5.5.0'} -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/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5 (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5 (1).eb deleted file mode 100644 index e1a049a993..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-ictce-6.2.5 (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': 'ictce', 'version': '6.2.5'} -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/gsl (Case Conflict)/GSL-1.16-intel-2014b (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b (1).eb deleted file mode 100644 index f93fbb1090..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2014b (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': '2014b'} -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/gsl (Case Conflict)/GSL-1.16-intel-2015a (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a (1).eb deleted file mode 100644 index 207992d0eb..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015a (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': '2015a'} -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/gsl (Case Conflict)/GSL-1.16-intel-2015b (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b (1).eb deleted file mode 100644 index 33c068c25d..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2015b (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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': '2015b'} -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/gsl (Case Conflict)/GSL-1.16-intel-2016a (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a (1).eb deleted file mode 100644 index aaffd974f5..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-1.16-intel-2016a (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '1.16' - -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 = {'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/gsl (Case Conflict)/GSL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-CrayGNU-2015.11.eb deleted file mode 100644 index 378ea5f63e..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-CrayGNU-2015.11.eb +++ /dev/null @@ -1,24 +0,0 @@ -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': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -sanity_check_paths={ - 'files': ['lib/libgsl.so', 'lib/libgsl.a'], - 'dirs': ['include'], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b (1).eb deleted file mode 100644 index 64966f0023..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2015b (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -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 = {'version': '2015b', 'name': 'foss'} -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/gsl (Case Conflict)/GSL-2.1-foss-2016a (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a (1).eb deleted file mode 100644 index f4a28c0d8f..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-foss-2016a (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -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 = {'version': '2016a', 'name': 'foss'} -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/gsl (Case Conflict)/GSL-2.1-intel-2015b (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b (1).eb deleted file mode 100644 index d363055a95..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2015b (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -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': '2015b'} -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/gsl (Case Conflict)/GSL-2.1-intel-2016a (1).eb b/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a (1).eb deleted file mode 100644 index 6ff19555c3..0000000000 --- a/easybuild/easyconfigs/g/gsl (Case Conflict)/GSL-2.1-intel-2016a (1).eb +++ /dev/null @@ -1,19 +0,0 @@ -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': '2016a'} -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 (Case Conflict)/Guile-2.0.11-foss-2016a.eb b/easybuild/easyconfigs/g/guile (Case Conflict)/Guile-2.0.11-foss-2016a.eb deleted file mode 100644 index 94a0abd7af..0000000000 --- a/easybuild/easyconfigs/g/guile (Case Conflict)/Guile-2.0.11-foss-2016a.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Guile' -version = '2.0.11' - -homepage = 'https://www.gnu.org/software/guile/' -description = """Guile is a programming language, designed to help programmers create flexible applications that - can be extended by users or other programmers with plug-ins, modules, or scripts.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -builddependencies = [('Autotools', '20150215')] -dependencies = [ - ('libunistring', '0.9.3'), - ('libffi', '3.2.1'), - ('gc', '7.4.4'), - ('GMP', '6.1.0'), -] - -sanity_check_paths = { - 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', 'bin/guile-snarf', 'bin/guile-tools', - 'include/guile/%(version_major_minor)s/libguile.h', - 'lib/libguile-%(version_major_minor)s.a', 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], - 'dirs': ['include/guile/%(version_major_minor)s/libguile', 'lib/guile/%(version_major_minor)s/ccache'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb similarity index 100% rename from easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503.eb rename to easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb diff --git a/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503 (1).eb b/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503 (1).eb deleted file mode 100644 index 7235621e5d..0000000000 --- a/easybuild/easyconfigs/m/mawk (Case Conflict)/Mawk-1.3.4-goolf-1.4.10-20150503 (1).eb +++ /dev/null @@ -1,27 +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 = 'ConfigureMake' - -name = 'Mawk' -version = '1.3.4' -versionsuffix = '-20150503' - -homepage = 'http://invisible-island.net/mawk/' -description = """mawk is an interpreter for the AWK Programming Language.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -source_urls = ['ftp://invisible-island.net/mawk/'] -sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/mawk'], - 'dirs': [], -} - -moduleclass = 'tools' -- 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 016/350] 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 30aeff37fd7f644e76061214cb1d5e6cb248dc7e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 26 Jul 2016 23:40:05 +0800 Subject: [PATCH 017/350] 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 018/350] 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 019/350] 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 020/350] 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 021/350] 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 509e62930698f749229af31253e522095c6455bb Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 Aug 2016 12:01:41 +0800 Subject: [PATCH 022/350] 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 56a7b4486807e1e494f420caeef02e1a17b814ba Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Thu, 11 Aug 2016 16:36:12 +0400 Subject: [PATCH 023/350] adding anaconda --- .../easyconfigs/a/Anaconda/anaconda-2.4.0.eb | 41 +++++++++++++++++++ .../easyconfigs/a/Anaconda/anaconda-3.4.0.eb | 39 ++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb create mode 100644 easybuild/easyconfigs/a/Anaconda/anaconda-3.4.0.eb diff --git a/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb new file mode 100644 index 0000000000..852014e264 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Authors:: Jillian Rowe +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_anaconda' + +name = "anaconda" +version = "2-4.0.0" +variant = "Linux-x86_64" + +homepage = "https://www.continuum.io/" +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +anaconda_version = 2 + +source_urls = ["http://repo.continuum.io/archive/"] +sources = ["Anaconda%s-%s.sh" % (version, variant)] +checksums = [ '31ed3ef07435d7068e1e03be49381b13' ] + +license_file = 'LICENSE.txt' + +sanity_check_paths = { + 'files': ['bin/pydoc', 'bin/2to3', 'bin/activate', 'bin/conda', 'bin/deactivate', 'bin/ipython', 'bin/sqlite3'], + 'dirs': ['bin', 'etc', 'lib', 'pkgs'] +} + +modextravars = { + 'ANACONDA_LICENSE': license_file, +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda/anaconda-3.4.0.eb b/easybuild/easyconfigs/a/Anaconda/anaconda-3.4.0.eb new file mode 100644 index 0000000000..9e2354b0de --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda/anaconda-3.4.0.eb @@ -0,0 +1,39 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Authors:: Jillian Rowe +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_anaconda' + +name = "anaconda" +version = "3-4.0.0" +variant = "Linux-x86_64" + +homepage = "https://www.continuum.io/" +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ["http://repo.continuum.io/archive/"] +sources = ["Anaconda%s-%s.sh" % (version, variant)] +checksums = ["546d1f02597587c685fa890c1d713b51"] + +license_file = 'LICENSE.txt' + +sanity_check_paths = { + 'files': ['bin/pydoc', 'bin/2to3', 'bin/activate', 'bin/conda', 'bin/deactivate', 'bin/ipython', 'bin/sqlite3'], + 'dirs': ['bin', 'etc', 'lib', 'pkgs'] +} + +modextravars = { + 'ANACONDA_LICENSE': license_file, +} + +moduleclass = 'lang' -- GitLab From 8636dc775f77fca955d26a3115217a34ed189545 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Thu, 11 Aug 2016 16:36:57 +0400 Subject: [PATCH 024/350] adding condacreate --- .../c/CondaCreate/condacreate-1.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb diff --git a/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb b/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb new file mode 100644 index 0000000000..378b53a6e2 --- /dev/null +++ b/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_CondaCreate' + +name = "condacreate-module" +version = "1.0" +variant = "Linux-x86_64" + +homepage = "https://github.com/bioconda/bioconda-recipes" +description = """ Conda is a platform- and + language-independent package manager that sports + easy distribution, installation and version + management of software. The bioconda channel is a + Conda channel providing bioinformatics related + packages. This repository hosts the corresponding + recipes. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +requirements = "perl-app-cpanminus" +channels = 'bioconda' +post_install_cmd = "cpanm --notest ExtUtils::MakeMaker" + +builddependencies = [('anaconda', '2-4.0.0')] + +sanity_check_paths = { + 'files': ['bin/cpanm', 'bin/perl'], + 'dirs': ['lib', 'lib/perl5'] +} + +moduleclass = 'tools' -- GitLab From 9e637e2d4515e1a409fa635b45556c1273ee593f Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Thu, 11 Aug 2016 16:37:44 +0400 Subject: [PATCH 025/350] commiting conda env --- .../easyconfigs/c/CondaEnv/condaenv-1.0.eb | 43 +++++++++++++++++++ .../easyconfigs/c/CondaEnv/environment.yml | 5 +++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb create mode 100644 easybuild/easyconfigs/c/CondaEnv/environment.yml diff --git a/easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb b/easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb new file mode 100644 index 0000000000..1a36b74954 --- /dev/null +++ b/easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb @@ -0,0 +1,43 @@ +## +# 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_CondaEnv' + +name = "condaenv-module" +version = "1.0" +variant = "Linux-x86_64" + +homepage = "https://github.com/bioconda/bioconda-recipes" +description = """ Conda is a platform- and + language-independent package manager that sports + easy distribution, installation and version + management of software. The bioconda channel is a + Conda channel providing bioinformatics related + packages. This repository hosts the corresponding + recipes. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +builddependencies = [('anaconda', '2-4.0.0')] + +#Use one of the following - either an environment.yml file or a remote environment definition +#sources = ["environment.yml"] +#environment = sources[0] + +remote_environment = "vader/deathstar" + +sanity_check_paths = { + 'files': ["bin/conda"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CondaEnv/environment.yml b/easybuild/easyconfigs/c/CondaEnv/environment.yml new file mode 100644 index 0000000000..d98bf281fe --- /dev/null +++ b/easybuild/easyconfigs/c/CondaEnv/environment.yml @@ -0,0 +1,5 @@ +name: variant_test +channels: + - bioconda +dependencies: + - samtools=1.3.1 -- 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 026/350] 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 9cebb8b6fdef1086b728a1d9c895c4f97a27430d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 19 Aug 2016 11:37:07 +0200 Subject: [PATCH 027/350] If system Qt4 is installed, wrong MOC used --- easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb index bf4776d474..e136d733e5 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -46,7 +46,7 @@ dependencies = [ ('GraphicsMagick', '1.3.23'), ] -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +configopts = 'MOC=$EBROOTQT/bin/moc --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' sanity_check_paths = { 'files': ['bin/octave'], -- GitLab From 5ee164092af292afaf17a0ae15fbea092cd2a301 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 29 Aug 2016 18:18:25 +0200 Subject: [PATCH 028/350] Create eb file for libxml2-2.9.2-goolf-1.5.16.eb --- .../l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb 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 new file mode 100644 index 0000000000..54c5dad803 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +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 3cf653b0ff9e6eae6512146536dd67051fd6c7ed Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 29 Aug 2016 17:45:26 +0200 Subject: [PATCH 029/350] Create eb files for libxslt for goolf-1.5.16 and foss-2016a --- .../l/libxslt/libxslt-1.1.28-foss-2016a.eb | 24 +++++++++++++++++++ .../l/libxslt/libxslt-1.1.28-goolf-1.5.16.eb | 23 ++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb new file mode 100644 index 0000000000..6b593148b4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-goolf-1.5.16.eb new file mode 100644 index 0000000000..ac1786bdfd --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-goolf-1.5.16.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/', +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.2'), +] + +moduleclass = 'lib' -- GitLab From cbe8ca0d477d063367672fbe537e722534a7c86f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 29 Aug 2016 17:38:39 +0200 Subject: [PATCH 030/350] Create eb files for XMLStarlet --- .../XMLStarlet/XMLStarlet-1.6.1-foss-2016a.eb | 26 +++++++++++++++++++ .../XMLStarlet-1.6.1-goolf-1.5.16.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-foss-2016a.eb create mode 100644 easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-foss-2016a.eb b/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-foss-2016a.eb new file mode 100644 index 0000000000..2179e09197 --- /dev/null +++ b/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XMLStarlet' +version = '1.6.1' + +homepage = 'http://xmlstar.sourceforge.net' +description = """Command line XML tool""" + + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [('http://sourceforge.net/projects/xmlstar/files/%s/%s' % (name.lower(), version), 'download')] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxml2', '2.9.3'), + ('libxslt', '1.1.28') +] + +sanity_check_paths = { + 'files': ['bin/xml', 'share/doc/xmlstarlet/html.css', 'share/doc/xmlstarlet/xmlstarlet-ug.html', + 'share/doc/xmlstarlet/xmlstarlet.txt', 'share/man/man1/xmlstarlet.1'], + 'dirs': ['bin', 'share/doc/xmlstarlet', 'share/man/man1'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-goolf-1.5.16.eb b/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-goolf-1.5.16.eb new file mode 100644 index 0000000000..552256c88b --- /dev/null +++ b/easybuild/easyconfigs/x/XMLStarlet/XMLStarlet-1.6.1-goolf-1.5.16.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XMLStarlet' +version = '1.6.1' + +homepage = 'http://xmlstar.sourceforge.net' +description = """Command line XML tool""" + + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = [('http://sourceforge.net/projects/xmlstar/files/%s/%s' % (name.lower(), version), 'download')] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libxml2', '2.9.2'), + ('libxslt', '1.1.28') +] + +sanity_check_paths = { + 'files': ['bin/xml', 'share/doc/xmlstarlet/html.css', 'share/doc/xmlstarlet/xmlstarlet-ug.html', + 'share/doc/xmlstarlet/xmlstarlet.txt', 'share/man/man1/xmlstarlet.1'], + 'dirs': ['bin', 'share/doc/xmlstarlet', 'share/man/man1'] +} + +moduleclass = 'data' -- GitLab From 1886526cf3746ffc8d61cf1a95de7eb517abc907 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 30 Aug 2016 05:06:19 +0400 Subject: [PATCH 031/350] updating condaenv config --- easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb b/easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb index 1a36b74954..ca01537d2c 100644 --- a/easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb +++ b/easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb @@ -31,9 +31,10 @@ builddependencies = [('anaconda', '2-4.0.0')] #Use one of the following - either an environment.yml file or a remote environment definition #sources = ["environment.yml"] -#environment = sources[0] +#It is not necessary to specify your environment_file unless it is named something besides environment.yml +#environment_file = sources[0] -remote_environment = "vader/deathstar" +remote_environment = "jerowe/gencore_python_1.0" sanity_check_paths = { 'files': ["bin/conda"], -- GitLab From b8e57e3328a14efdee37f00114c7197fee189e68 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 30 Aug 2016 05:10:03 +0400 Subject: [PATCH 032/350] updating anaconda 2 to remove anaconda_version --- easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb index 852014e264..8251c357ce 100644 --- a/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb +++ b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb @@ -21,8 +21,6 @@ that empowers companies to adopt a modern open data science analytics architectu toolchain = {'name': 'dummy', 'version': 'dummy'} -anaconda_version = 2 - source_urls = ["http://repo.continuum.io/archive/"] sources = ["Anaconda%s-%s.sh" % (version, variant)] checksums = [ '31ed3ef07435d7068e1e03be49381b13' ] -- GitLab From b5299437a92fe3312d002c7c19af81e77e9263d2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 7 Sep 2016 11:11:15 +0200 Subject: [PATCH 033/350] 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 b53b2802faf0fa4e37760c3542fe3d458d6e4a0c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 9 Sep 2016 10:55:58 +0800 Subject: [PATCH 034/350] 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 035/350] 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 1815dfecf67ec275c3873cd88a2985c845759e90 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 10 Sep 2016 11:54:12 +0800 Subject: [PATCH 036/350] 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 9fee61323514bdbe0dc8792da18538ab70e7b60e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 16 Sep 2016 10:15:34 +0200 Subject: [PATCH 037/350] 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 038/350] 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 6f64c98d078beb5de89e99519729587d742c7895 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 16 Sep 2016 12:42:44 +0200 Subject: [PATCH 039/350] 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 040/350] 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 041/350] 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 042/350] 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 f0a42c7edd985a11ee0ae5037e75758d01450452 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 19 Sep 2016 14:02:03 +0200 Subject: [PATCH 043/350] 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 044/350] 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 a68f490cb9cd1d1ebcb4f2b489df724f9d76e3ac Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 20 Sep 2016 15:07:51 +0200 Subject: [PATCH 045/350] 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 046/350] 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 047/350] 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 048/350] 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 e66be064481fe46e047d50e20e275ec9412d3b98 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 21 Sep 2016 12:04:20 +0800 Subject: [PATCH 049/350] 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 8fe44ea98e79db6759715c96ad327c8caf32e77e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 22 Sep 2016 15:58:42 +0800 Subject: [PATCH 050/350] 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 5967479a1f949dad7bb3a8fa65f26450053a6232 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 23 Sep 2016 14:41:29 +0200 Subject: [PATCH 051/350] 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 052/350] 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 053/350] 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 054/350] 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 055/350] 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 056/350] 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 057/350] 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 058/350] 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 059/350] 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 060/350] 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 061/350] 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 062/350] 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 063/350] 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 064/350] 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 065/350] 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 066/350] 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 067/350] 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 068/350] 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 069/350] 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 070/350] 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 071/350] 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 072/350] 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 073/350] 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 074/350] 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 a51d6217a425f50a94de4f0af71b03167cf54dc4 Mon Sep 17 00:00:00 2001 From: Sergey Paramonov Date: Tue, 27 Sep 2016 14:36:37 -0400 Subject: [PATCH 075/350] Update GCCcore-5.4.0.eb * added original source url for Integer Set Library (isl-0.15.tar.bz2) --- easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index 5b9a17485e..ac9aa8567c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -18,6 +18,7 @@ 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://isl.gforge.inria.fr/', # original HTTP source for ISL (isl-0.15.tar.bz2) dependency ] sources = [ -- 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 076/350] 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 077/350] 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 7d62fe3c2d673e05213344c5c33ea95e84b771dc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Sep 2016 10:38:04 +0200 Subject: [PATCH 078/350] Added atools/1.4 --- .../atools-1.4-intel-2016b-Python-2.7.12.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/a/atools/atools-1.4-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/atools/atools-1.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/atools/atools-1.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..72ce8bce28 --- /dev/null +++ b/easybuild/easyconfigs/a/atools/atools-1.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'atools' +version = '1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/gjbex/atools' +description = """Tools to make using job arrays a lot more convenient.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/gjbex/atools/archive'] + +builddependencies = [('Autotools', '20150215')] + +dependencies = [('Python', '2.7.12')] + +preconfigopts = 'autoreconf -v -f && ' + +sanity_check_paths = { + 'files': ['bin/aenv', 'bin/alog', 'bin/arange'], + 'dirs': ['lib/vsc/atools'] +} + +moduleclass = 'tools' -- GitLab From 064c17eae2b16d2d24c008de25aabe886851fb50 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Sep 2016 14:32:04 +0200 Subject: [PATCH 079/350] 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 080/350] 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 081/350] 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 082/350] 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 d7660f8041eaf32c724da64e20825203f674bab7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 29 Sep 2016 13:37:29 +0200 Subject: [PATCH 083/350] Use newer version with bugfixes --- ...-2.7.12.eb => atools-1.4.1-intel-2016b-Python-2.7.12.eb} | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) rename easybuild/easyconfigs/a/atools/{atools-1.4-intel-2016b-Python-2.7.12.eb => atools-1.4.1-intel-2016b-Python-2.7.12.eb} (82%) diff --git a/easybuild/easyconfigs/a/atools/atools-1.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/atools/atools-1.4.1-intel-2016b-Python-2.7.12.eb similarity index 82% rename from easybuild/easyconfigs/a/atools/atools-1.4-intel-2016b-Python-2.7.12.eb rename to easybuild/easyconfigs/a/atools/atools-1.4.1-intel-2016b-Python-2.7.12.eb index 72ce8bce28..990feda7cf 100644 --- a/easybuild/easyconfigs/a/atools/atools-1.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/atools/atools-1.4.1-intel-2016b-Python-2.7.12.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'atools' -version = '1.4' +version = '1.4.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/gjbex/atools' @@ -12,12 +12,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/gjbex/atools/archive'] -builddependencies = [('Autotools', '20150215')] - dependencies = [('Python', '2.7.12')] -preconfigopts = 'autoreconf -v -f && ' - sanity_check_paths = { 'files': ['bin/aenv', 'bin/alog', 'bin/arange'], 'dirs': ['lib/vsc/atools'] -- GitLab From c0689e183458a437e5b26fd910784e0ee11ce66e Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 29 Sep 2016 14:57:41 +0200 Subject: [PATCH 084/350] 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 085/350] 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 9da2ed856a9f371e88ae964c778f4227b8bea6ea Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 29 Sep 2016 15:59:18 +0200 Subject: [PATCH 086/350] Extra version bump to include missing makefile.in --- ...thon-2.7.12.eb => atools-1.4.2-intel-2016b-Python-2.7.12.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/atools/{atools-1.4.1-intel-2016b-Python-2.7.12.eb => atools-1.4.2-intel-2016b-Python-2.7.12.eb} (96%) diff --git a/easybuild/easyconfigs/a/atools/atools-1.4.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/atools/atools-1.4.2-intel-2016b-Python-2.7.12.eb similarity index 96% rename from easybuild/easyconfigs/a/atools/atools-1.4.1-intel-2016b-Python-2.7.12.eb rename to easybuild/easyconfigs/a/atools/atools-1.4.2-intel-2016b-Python-2.7.12.eb index 990feda7cf..3f41851d67 100644 --- a/easybuild/easyconfigs/a/atools/atools-1.4.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/atools/atools-1.4.2-intel-2016b-Python-2.7.12.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'atools' -version = '1.4.1' +version = '1.4.2' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/gjbex/atools' -- GitLab From 6f07b0f101826b36fbdcb3995f0157f42aef2efe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 30 Sep 2016 09:38:39 +0200 Subject: [PATCH 087/350] 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 088/350] {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 089/350] {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 090/350] 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 091/350] 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 092/350] {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 093/350] 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 094/350] 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 095/350] 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 8ac426ebbaad4a55600905316877fd35ea411565 Mon Sep 17 00:00:00 2001 From: Eliot Eshelman Date: Wed, 24 Aug 2016 21:08:08 -0400 Subject: [PATCH 096/350] Add a toolchain for foss/2016a + NVIDIA CUDA 7.5 --- .../c/CUDA/CUDA-7.5.18-GCC-4.9.3-2.25.eb | 33 ++++++++++++ .../f/FFTW/FFTW-3.3.4-gompic-2016.08.eb | 34 +++++++++++++ .../easyconfigs/g/gcccuda/gcccuda-2016.08.eb | 21 ++++++++ .../easyconfigs/g/gompic/gompic-2016.08.eb | 23 +++++++++ .../easyconfigs/g/goolfc/goolfc-2016.08.eb | 38 ++++++++++++++ .../h/hwloc/hwloc-1.11.2-gcccuda-2016.08.eb | 19 +++++++ ...BLAS-0.2.15-gompic-2016.08-LAPACK-3.6.0.eb | 51 +++++++++++++++++++ .../OpenMPI/OpenMPI-1.10.2-gcccuda-2016.08.eb | 32 ++++++++++++ ...ic-2016.08-OpenBLAS-0.2.15-LAPACK-3.6.0.eb | 25 +++++++++ 9 files changed, 276 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb create mode 100644 easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb create mode 100644 easybuild/easyconfigs/g/gompic/gompic-2016.08.eb create mode 100644 easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-gcccuda-2016.08.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-gompic-2016.08-LAPACK-3.6.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-gcccuda-2016.08.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.15-LAPACK-3.6.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..13983fecee --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.3-2.25.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA, Ghent University, Microway +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste, Eliot Eshelman +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +name = 'CUDA' +version = '7.5.18' + +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': '4.9.3-2.25'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] +checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] + +# Necessary to allow to use a GCC 4.9.3 toolchain, as CUDA by default just supports up to 4.9.2. +# Tested, but not throughly, so it is not guaranteed to don't cause problems +installopts = '-override compiler' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb new file mode 100644 index 0000000000..59828cee2d --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.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': 'gompic', 'version': '2016.08'} +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/g/gcccuda/gcccuda-2016.08.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb new file mode 100644 index 0000000000..9572b6a58a --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2016.08' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '4.9.3-2.25' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('CUDA', '7.5.18', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb b/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb new file mode 100644 index 0000000000..d75cda72fc --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2016.08' + +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 = '4.9.3-2.25' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, # part of gcccuda + ('CUDA', '7.5.18', '', comp), # part of gcccuda + ('OpenMPI', '1.10.2', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb new file mode 100644 index 0000000000..0a4b029820 --- /dev/null +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb @@ -0,0 +1,38 @@ +easyblock = "Toolchain" + +name = 'goolfc' +version = '2016.08' + +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 = '4.9.3-2.25' +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 = '0.2.15' +blassuff = '-LAPACK-3.6.0' +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', '7.5.18', '', comp), # part of gompic + ('OpenMPI', '1.10.2', '', ('gcccuda', version)), # part of gompic + (blaslib, blasver, blassuff, comp_mpi_tc), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-gcccuda-2016.08.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-gcccuda-2016.08.eb new file mode 100644 index 0000000000..67cdded106 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-gcccuda-2016.08.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = "1.11.2" + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'gcccuda', 'version': '2016.08'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-gompic-2016.08-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-gompic-2016.08-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..8343b91415 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-gompic-2016.08-LAPACK-3.6.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.15' + +lapackver = '3.6.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'gompic', 'version': '2016.08'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-gcccuda-2016.08.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-gcccuda-2016.08.eb new file mode 100644 index 0000000000..050c6e7be0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-gcccuda-2016.08.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = "1.10.2" + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'gcccuda', 'version': '2016.08'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.2')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$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_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-gompic-2016.08-OpenBLAS-0.2.15-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.15-LAPACK-3.6.0.eb new file mode 100644 index 0000000000..f7b5313129 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.15-LAPACK-3.6.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompic', 'version': '2016.08'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.15' +blassuff = '-LAPACK-3.6.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.3-2.25'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 630b5d7a28e4241b41d45e14081c309a41722416 Mon Sep 17 00:00:00 2001 From: Eliot Eshelman Date: Mon, 3 Oct 2016 21:46:34 -0400 Subject: [PATCH 097/350] No need for optarch, as it is enabled by default --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb index 59828cee2d..283a4b3d0d 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompic-2016.08.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': 'gompic', 'version': '2016.08'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] -- GitLab From d147126da37690dd9b13689f61760aa3e9beffdc Mon Sep 17 00:00:00 2001 From: Eliot Eshelman Date: Tue, 4 Oct 2016 22:34:48 -0400 Subject: [PATCH 098/350] Update versions as suggested by EasyBuild team --- ...5.18-GCC-4.9.3-2.25.eb => CUDA-7.5.18-GCC-4.9.4-2.25.eb} | 4 ++-- easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb | 2 +- easybuild/easyconfigs/g/gompic/gompic-2016.08.eb | 4 ++-- easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb | 6 +++--- ...2-gcccuda-2016.08.eb => hwloc-1.11.3-gcccuda-2016.08.eb} | 2 +- ....0.eb => OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb} | 4 ++-- ...gcccuda-2016.08.eb => OpenMPI-1.10.3-gcccuda-2016.08.eb} | 4 ++-- ...CK-2.0.2-gompic-2016.08-OpenBLAS-0.2.18-LAPACK-3.6.0.eb} | 4 ++-- 8 files changed, 15 insertions(+), 15 deletions(-) rename easybuild/easyconfigs/c/CUDA/{CUDA-7.5.18-GCC-4.9.3-2.25.eb => CUDA-7.5.18-GCC-4.9.4-2.25.eb} (91%) rename easybuild/easyconfigs/h/hwloc/{hwloc-1.11.2-gcccuda-2016.08.eb => hwloc-1.11.3-gcccuda-2016.08.eb} (97%) rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.2.15-gompic-2016.08-LAPACK-3.6.0.eb => OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb} (95%) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-1.10.2-gcccuda-2016.08.eb => OpenMPI-1.10.3-gcccuda-2016.08.eb} (95%) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.15-LAPACK-3.6.0.eb => ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.18-LAPACK-3.6.0.eb} (87%) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb similarity index 91% rename from easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.3-2.25.eb rename to easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb index 13983fecee..eecde07096 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb @@ -19,14 +19,14 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall 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': '4.9.3-2.25'} +toolchain = {'name': 'GCC', 'version': '4.9.4-2.25'} source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_linux.run'] checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] -# Necessary to allow to use a GCC 4.9.3 toolchain, as CUDA by default just supports up to 4.9.2. +# Necessary to allow to use a GCC 4.9.4 toolchain, as CUDA by default just supports up to 4.9.2. # Tested, but not throughly, so it is not guaranteed to don't cause problems installopts = '-override compiler' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb index 9572b6a58a..18f71c6334 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb @@ -9,7 +9,7 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, along w toolchain = {'name': 'dummy', 'version': 'dummy'} comp_name = 'GCC' -comp_ver = '4.9.3-2.25' +comp_ver = '4.9.4-2.25' comp = (comp_name, comp_ver) # compiler toolchain dependencies diff --git a/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb b/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb index d75cda72fc..1afeb092c2 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb @@ -10,14 +10,14 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain along wi toolchain = {'name': 'dummy', 'version': 'dummy'} comp_name = 'GCC' -comp_ver = '4.9.3-2.25' +comp_ver = '4.9.4-2.25' comp = (comp_name, comp_ver) # compiler toolchain dependencies dependencies = [ comp, # part of gcccuda ('CUDA', '7.5.18', '', comp), # part of gcccuda - ('OpenMPI', '1.10.2', '', ('gcccuda', version)), + ('OpenMPI', '1.10.3', '', ('gcccuda', version)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb index 0a4b029820..1ae98dc94c 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb @@ -10,7 +10,7 @@ description = """GCC based compiler toolchain __with CUDA support__, and includi toolchain = {'name': 'dummy', 'version': 'dummy'} comp_name = 'GCC' -comp_ver = '4.9.3-2.25' +comp_ver = '4.9.4-2.25' comp = (comp_name, comp_ver) # toolchain used to build goolfc dependencies @@ -19,7 +19,7 @@ comp_mpi_tc_ver = version comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) blaslib = 'OpenBLAS' -blasver = '0.2.15' +blasver = '0.2.18' blassuff = '-LAPACK-3.6.0' blas = '-%s-%s%s' % (blaslib, blasver, blassuff) @@ -29,7 +29,7 @@ blas = '-%s-%s%s' % (blaslib, blasver, blassuff) dependencies = [ comp, # part of gompic ('CUDA', '7.5.18', '', comp), # part of gompic - ('OpenMPI', '1.10.2', '', ('gcccuda', version)), # part of gompic + ('OpenMPI', '1.10.3', '', ('gcccuda', version)), # part of gompic (blaslib, blasver, blassuff, comp_mpi_tc), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-gcccuda-2016.08.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb similarity index 97% rename from easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-gcccuda-2016.08.eb rename to easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb index 67cdded106..4a821b0537 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-gcccuda-2016.08.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' -version = "1.11.2" +version = "1.11.3" homepage = 'http://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-gompic-2016.08-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb similarity index 95% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-gompic-2016.08-LAPACK-3.6.0.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb index 8343b91415..5a0c375e93 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-gompic-2016.08-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'OpenBLAS' -version = '0.2.15' +version = '0.2.18' lapackver = '3.6.0' versionsuffix = '-LAPACK-%s' % lapackver @@ -9,7 +9,7 @@ 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': '2016.08'} +toolchain = {'name': 'GCC', 'version': '4.9.4-2.25'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-gcccuda-2016.08.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb similarity index 95% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-gcccuda-2016.08.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb index 050c6e7be0..917b152207 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-gcccuda-2016.08.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' -version = "1.10.2" +version = "1.10.3" homepage = 'http://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" @@ -11,7 +11,7 @@ toolchain = {'name': 'gcccuda', 'version': '2016.08'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -dependencies = [('hwloc', '1.11.2')] +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 diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.15-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.18-LAPACK-3.6.0.eb similarity index 87% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.15-LAPACK-3.6.0.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.18-LAPACK-3.6.0.eb index f7b5313129..daad463a99 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.15-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.08-OpenBLAS-0.2.18-LAPACK-3.6.0.eb @@ -12,12 +12,12 @@ source_urls = [homepage] sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' -blasver = '0.2.15' +blasver = '0.2.18' blassuff = '-LAPACK-3.6.0' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.3-2.25'))] +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.4-2.25'))] # parallel build tends to fail, so disabling it parallel = 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 099/350] 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 100/350] 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 101/350] 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 102/350] 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 103/350] 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 104/350] 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 105/350] 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 106/350] 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 107/350] 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=$MPICC' + +benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': benchmark_dirs, +} + +moduleclass = 'perf' -- GitLab From c067ea08def05b1d026da1f8aabc94ea9377487d Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 7 Oct 2016 16:13:12 +0200 Subject: [PATCH 108/350] IMB-4.1 with foss --- .../easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb new file mode 100644 index 0000000000..7c82e8b734 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """ +The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +prebuildopts = 'export MPI_HOME=$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 109/350] 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 110/350] 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 111/350] 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 112/350] 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 113/350] 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 114/350] 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 115/350] 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 53916c86db511b3da983c2fcac214b1490531118 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Oct 2016 10:52:51 +0200 Subject: [PATCH 116/350] add easyconfig OpenFOAM-3.0.1-intel-2016b.eb --- .../o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb new file mode 100644 index 0000000000..ca5d08b992 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '3.0.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major_minor)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['a6ffe3edabdd23f9eff31be47a092b07'] + +patches = ['OpenFOAM-3.0.0_cleanup.patch'] + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + # 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', '3.6.1'), + ('flex', '2.6.0'), +] + +moduleclass = 'cae' -- GitLab From 19600a8644c1836d4d0f8970112796f1ca5ffadc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 10 Oct 2016 11:39:27 +0200 Subject: [PATCH 117/350] {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 118/350] 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 ${MPI_HOME} -name mpicc -print) + -- GitLab From b1eb59353a12fd8be5aaa1db252e2537f92a033b Mon Sep 17 00:00:00 2001 From: RvDijk Date: Mon, 10 Oct 2016 12:06:09 +0200 Subject: [PATCH 119/350] double quotes --- .../OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb index 1bc3f774aa..d25cf1b3ab 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC=$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 ce55d128d7a4238e8819075a97dc3274f62d77f2 Mon Sep 17 00:00:00 2001 From: Eliot Eshelman Date: Mon, 10 Oct 2016 16:12:08 -0400 Subject: [PATCH 120/350] Use the correct toolchain for OpenBLAS --- easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb index 1ae98dc94c..82819f4c5e 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb @@ -30,7 +30,7 @@ dependencies = [ comp, # part of gompic ('CUDA', '7.5.18', '', comp), # part of gompic ('OpenMPI', '1.10.3', '', ('gcccuda', version)), # part of gompic - (blaslib, blasver, blassuff, comp_mpi_tc), + (blaslib, blasver, blassuff, comp), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), ] -- GitLab From 42a8ceaddf7751e4ac9cdfc36dc096aae0d39c39 Mon Sep 17 00:00:00 2001 From: Eliot Eshelman Date: Mon, 10 Oct 2016 16:12:57 -0400 Subject: [PATCH 121/350] Add EasyConfig for HPL on goolfc-2016.08 --- .../h/HPL/HPL-2.2-goolfc-2016.08.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb new file mode 100644 index 0000000000..d1430d0e3a --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.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': 'goolfc', 'version': '2016.08'} +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 b1e01ba7486d80d4d860df1af00d6172ef7d0c2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2016 11:23:03 +0200 Subject: [PATCH 122/350] 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 123/350] 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 124/350] {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 125/350] * 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 126/350] 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 127/350] 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 302ab073ba386b70234e0b5711c0961f5076aab7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 11 Oct 2016 12:55:20 +0200 Subject: [PATCH 128/350] Add easyconfigs for GROMACS 2016. Boost is only a build dep of Gromacs. Gromacs now contains tinyxml and thus do not depend on libxml2 any longer. --- .../GROMACS/GROMACS-2016-foss-2016b-hybrid.eb | 38 +++++++++++++++++++ .../g/GROMACS/GROMACS-2016-foss-2016b-mt.eb | 37 ++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb new file mode 100644 index 0000000000..781809d07e --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +# +# Version 5.1.4 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '2016' +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'), + ('Boost', '1.61.0'), +] + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb new file mode 100644 index 0000000000..b1fa93887b --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +# +# Version 5.1.4 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '2016' +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'), + ('Boost', '1.61.0'), +] + +moduleclass = 'bio' -- GitLab From 2933a74b36b309d5b7bfd3507f2a59c28125f363 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2016 12:57:38 +0200 Subject: [PATCH 129/350] 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 130/350] 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 131/350] 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 132/350] 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 133/350] {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 134/350] 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 135/350] {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 136/350] 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 137/350] 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 $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " cmds_map = [('stream.c', cmds_str)] -- GitLab From 0811eb9919de070f8f50c48384ed48dd294b0791 Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Wed, 12 Oct 2016 14:19:26 +0200 Subject: [PATCH 138/350] Actually install the binaries --- easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb index f0b6a78950..9205395e4e 100644 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb @@ -29,10 +29,10 @@ cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=500000000 cmds_map = [('stream.c', cmds_str)] -files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B'], 'bin')] +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] sanity_check_paths = { - 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B'], + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], 'dirs': [], } -- GitLab From 3581cedbcabb987eb94dae96eb0bb9baf4252d1f Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Wed, 12 Oct 2016 14:37:12 +0200 Subject: [PATCH 139/350] STREAM 5.10 with 2016b toolchain --- .../s/STREAM/STREAM-5.10-intel-2016b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb new file mode 100644 index 0000000000..94341c99a0 --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2016b.eb @@ -0,0 +1,41 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'http://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www.cs.virginia.edu/stream/FTP/Code/'] +sources = ['%(namelower)s.c'] +checksums = ['dd2941e3a28ff90a79b571273c10aacf'] + +skipsteps = ['source'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +cmds_str = "$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 $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream.c', cmds_str)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' -- GitLab From 3dea1fdaf88545ed609f75003f63611c9e5c2b24 Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Wed, 12 Oct 2016 15:07:40 +0200 Subject: [PATCH 140/350] 5B elements does not build with the 2015a toolchain --- easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb index 9205395e4e..44cf8f84ff 100644 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb @@ -24,15 +24,13 @@ cmds_str += "$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 $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " cmds_map = [('stream.c', cmds_str)] -files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B'], 'bin')] sanity_check_paths = { - 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B'], 'dirs': [], } -- GitLab From cea6e793fbff4661ed3a376dbb21ed456d27b539 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 12 Oct 2016 15:40:57 +0200 Subject: [PATCH 141/350] more requested changes --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 9 ++++----- easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch | 11 ----------- 2 files changed, 4 insertions(+), 16 deletions(-) delete mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1_make_mpich.patch diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index f47f929afb..09fb675534 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -5,7 +5,8 @@ version = '4.1' homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' description = """ -The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes. +The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point +and global communication operations for a range of message sizes. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -15,9 +16,7 @@ source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] start_dir = 'src' prebuildopts = 'export MPI_HOME=$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 142/350] 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 143/350] 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 144/350] 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 145/350] 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 146/350] 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 147/350] 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 148/350] 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 149/350] 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 150/350] 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 151/350] 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 152/350] 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 52156c3e2feff84afd71cf995427dc90905e130c Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 13 Oct 2016 14:19:34 +0200 Subject: [PATCH 153/350] Consistently use 'pic=True' toolchain option and M4 as a dependency --- .../easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb | 6 ++++++ .../f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb | 6 ++++++ easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb | 7 +++++++ .../f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb | 6 ++++++ easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb | 7 +++++++ .../f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb | 11 +++++++---- .../easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb | 11 +++++++---- .../easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb | 7 +++++++ .../easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-gimkl-2.11.5.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-ictce-7.1.2.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-intel-2014b.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-intel-2015a.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb | 6 ++++++ .../f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb | 6 ++++++ .../easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb | 6 ++++++ .../f/flex/flex-2.5.39-intel-para-2014.12.eb | 6 ++++++ easybuild/easyconfigs/f/flex/flex-2.5.39.eb | 6 +++++- 24 files changed, 148 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb index 24e3dfb5dc..0542fac499 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.06.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb index 8c57faa309..ce034a2f5d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-2015.11.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb index 98e5ff5527..ac2d9ea164 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -6,10 +6,16 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('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-2.5.39-GCC-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb index 1c15e90f19..6e01f166de 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2.eb @@ -6,8 +6,15 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb index 667f205b69..72d2805b5f 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -6,10 +6,16 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-2.25'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('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-2.5.39-GCC-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb index 034599b7bc..d5baf97d6d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3.eb @@ -6,8 +6,15 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '4.9.3'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb index 75d18ede78..facf8e7f13 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -6,10 +6,16 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-2.25'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('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-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb index 71675a8b5c..a28470817b 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -6,14 +6,17 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCCcore', 'version': '4.9.2'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -# use same binutils version that was used when building GCCcore toolchain -builddependencies = [ - ('M4', '1.4.17'), - ('binutils', '2.25', '', True) +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] +dependencies = [('M4', '1.4.17')] +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.25', '', True)] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index 32dffb057f..68344b21cb 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -6,14 +6,17 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -# use same binutils version that was used when building GCCcore toolchain -builddependencies = [ - ('M4', '1.4.17'), - ('binutils', '2.25', '', True) +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] +dependencies = [('M4', '1.4.17')] +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.25', '', True)] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb index 3b653b0adc..255450ebc9 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb @@ -6,8 +6,15 @@ description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb index 6a24b017aa..72f37c4db6 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb index 208a02e540..1ad0409c77 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb index f9226ff5f3..11968e1640 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb index 40befb9e4a..0e52dfb998 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb index 352bff8334..69470ed39a 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2016a.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-gimkl-2.11.5.eb index 0bebc72067..60bcff5315 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-gimkl-2.11.5.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-ictce-7.1.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-ictce-7.1.2.eb index dc6e43a06e..0f6d234b9e 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-ictce-7.1.2.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2014b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2014b.eb index a2a804a379..37e678754d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2014b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2014b.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015a.eb index 859df83543..7f2ee18cbd 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015a.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb index 159eef3274..c1b7ac5006 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb index 154963c1c8..5e00cb4b9a 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016.02-GCC-4.9.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb index 419266740d..de60e46854 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016a.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb index 7cd93ab5fc..09e533d59d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb @@ -11,4 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb index e4d83f163c..797f2faa4f 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -builddependencies = [('M4', '1.4.17')] +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.17')] moduleclass = 'lang' -- GitLab From 96460b378780675e6d6cb4ef6746987d8ee26529 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 13 Oct 2016 14:46:01 +0200 Subject: [PATCH 154/350] Add missing M4 dependency for foss-2015.05 toolchain --- .../m/M4/M4-1.4.17-foss-2015.05.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb new file mode 100644 index 0000000000..a244ff7f0d --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb @@ -0,0 +1,25 @@ +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': '2015.05'} + +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 = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 503ce8d6e0aff9a45b805e7923731ffa642c0060 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Oct 2016 14:40:10 +0200 Subject: [PATCH 155/350] rework Anaconda easyconfigs based on changes to Anaconda easyblock --- .../easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb | 19 +++++++++ .../easyconfigs/a/Anaconda/Anaconda3.4.0.0.eb | 19 +++++++++ .../easyconfigs/a/Anaconda/anaconda-2.4.0.eb | 39 ------------------- .../easyconfigs/a/Anaconda/anaconda-3.4.0.eb | 39 ------------------- 4 files changed, 38 insertions(+), 78 deletions(-) create mode 100644 easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb create mode 100644 easybuild/easyconfigs/a/Anaconda/Anaconda3.4.0.0.eb delete mode 100644 easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb delete mode 100644 easybuild/easyconfigs/a/Anaconda/anaconda-3.4.0.eb diff --git a/easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb b/easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb new file mode 100644 index 0000000000..b5ffaf0935 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb @@ -0,0 +1,19 @@ +# author: Jillian Rowe +easyblock = 'EB_Anaconda' + +name = 'Anaconda2' +version = '4.0.0' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://repo.continuum.io/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['31ed3ef07435d7068e1e03be49381b13' ] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda/Anaconda3.4.0.0.eb b/easybuild/easyconfigs/a/Anaconda/Anaconda3.4.0.0.eb new file mode 100644 index 0000000000..9d77e1debf --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda/Anaconda3.4.0.0.eb @@ -0,0 +1,19 @@ +# author: Jillian Rowe +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '4.0.0' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://repo.continuum.io/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['546d1f02597587c685fa890c1d713b51'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb b/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb deleted file mode 100644 index 8251c357ce..0000000000 --- a/easybuild/easyconfigs/a/Anaconda/anaconda-2.4.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# -# Authors:: Jillian Rowe -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_anaconda' - -name = "anaconda" -version = "2-4.0.0" -variant = "Linux-x86_64" - -homepage = "https://www.continuum.io/" -description = """Built to complement the rich, open source Python community, -the Anaconda platform provides an enterprise-ready data analytics platform -that empowers companies to adopt a modern open data science analytics architecture. -""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ["http://repo.continuum.io/archive/"] -sources = ["Anaconda%s-%s.sh" % (version, variant)] -checksums = [ '31ed3ef07435d7068e1e03be49381b13' ] - -license_file = 'LICENSE.txt' - -sanity_check_paths = { - 'files': ['bin/pydoc', 'bin/2to3', 'bin/activate', 'bin/conda', 'bin/deactivate', 'bin/ipython', 'bin/sqlite3'], - 'dirs': ['bin', 'etc', 'lib', 'pkgs'] -} - -modextravars = { - 'ANACONDA_LICENSE': license_file, -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda/anaconda-3.4.0.eb b/easybuild/easyconfigs/a/Anaconda/anaconda-3.4.0.eb deleted file mode 100644 index 9e2354b0de..0000000000 --- a/easybuild/easyconfigs/a/Anaconda/anaconda-3.4.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# -# Authors:: Jillian Rowe -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_anaconda' - -name = "anaconda" -version = "3-4.0.0" -variant = "Linux-x86_64" - -homepage = "https://www.continuum.io/" -description = """Built to complement the rich, open source Python community, -the Anaconda platform provides an enterprise-ready data analytics platform -that empowers companies to adopt a modern open data science analytics architecture. -""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ["http://repo.continuum.io/archive/"] -sources = ["Anaconda%s-%s.sh" % (version, variant)] -checksums = ["546d1f02597587c685fa890c1d713b51"] - -license_file = 'LICENSE.txt' - -sanity_check_paths = { - 'files': ['bin/pydoc', 'bin/2to3', 'bin/activate', 'bin/conda', 'bin/deactivate', 'bin/ipython', 'bin/sqlite3'], - 'dirs': ['bin', 'etc', 'lib', 'pkgs'] -} - -modextravars = { - 'ANACONDA_LICENSE': license_file, -} - -moduleclass = 'lang' -- GitLab From 483a61dffd1abe479da14723461a506898be1b0e Mon Sep 17 00:00:00 2001 From: Andy Georges Date: Thu, 13 Oct 2016 14:53:45 +0200 Subject: [PATCH 156/350] 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 157/350] 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 158/350] 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 159/350] 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 $root/bin/compilervars.sh" -} -''' - - -license_file = '/gpfs/apps/intel/LicenseManager/current/INTEL.lic' +components = ['intel-mkl'] interfaces = True -moduleclass = 'numlib' +license_file = HOME + '/licenses/intel/license.lic' postinstallcmds = [ # extract the examples @@ -44,5 +30,7 @@ postinstallcmds = [ ] modextravars = { - 'MKL_EXAMPLES' : '%(installdir)s/mkl/examples/', + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', } + +moduleclass = 'numlib' -- GitLab From 30993ba3a23df3400223e079cdf4d1b7b61b8db5 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Thu, 13 Oct 2016 15:13:29 +0100 Subject: [PATCH 160/350] Updating OpenMPI to be like similar files on upstream --- ...10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 20 +++++++++---------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 5de853b009..2320c2ab64 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -9,23 +9,20 @@ description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -configopts += '--with-hwloc=/usr/local/packages/hwloc ' # hwloc support +configopts += '--with-hwloc=$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 183c2b982da67c49c162a9a1cca00a9c6ac010e2 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Thu, 13 Oct 2016 15:50:02 +0100 Subject: [PATCH 161/350] Amber 16 support for serial, MPI and CUDA builds - including all deps --- .../a/Amber/Amber-16-iomkl-2016.07-serial.eb | 32 ++++ .../a/Amber/Amber-16-iomkl-2016.07.eb | 32 ++++ ...er-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb | 32 ++++ ...oconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb | 26 ++++ ...omake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb | 36 +++++ ...s-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb | 17 +++ ...ison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb | 22 +++ ...zip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb | 15 ++ ...Make-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb | 31 ++++ ...5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 45 ++++++ ...URL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 31 ++++ ...gen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 19 +++ ...lex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb | 14 ++ .../GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 30 ++++ ...DF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb | 23 +++ ...adline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb | 32 ++++ ...tool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb | 17 +++ .../M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb | 23 +++ ...curses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 34 +++++ ...DF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb | 20 +++ ...tCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 35 +++++ ...SSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb | 19 +++ ...hon-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 137 ++++++++++++++++++ ...Lite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 43 ++++++ .../Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb | 23 +++ .../Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb | 25 ++++ .../Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb | 26 ++++ ...zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb | 22 +++ 28 files changed, 861 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb new file mode 100644 index 0000000000..35516d3232 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb @@ -0,0 +1,32 @@ +# +# Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +# +name = 'Amber' +version = '16' +ambertools_ver = '16' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (5, 14) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' %(ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'usempi': False} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] + +dependencies = [ + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +patches = ['Amber-16_fix-hardcoding.patch'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb new file mode 100644 index 0000000000..4551ed1bc9 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb @@ -0,0 +1,32 @@ +# +# Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +# +name = 'Amber' +version = '16' +ambertools_ver = '16' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (5, 14) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' %(ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'usempi': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] + +dependencies = [ + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +patches = ['Amber-16_fix-hardcoding.patch'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb new file mode 100644 index 0000000000..a2cab13af2 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb @@ -0,0 +1,32 @@ +# Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +# +name = 'Amber' +version = '16' +ambertools_ver = '16' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (5, 14) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' %(ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'usempi': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] + +dependencies = [ + ('CUDA', '7.5.18', '', ('iccifort', '2016.3.210-GCC-4.9.3-2.25')), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +patches = ['Amber-16_fix-hardcoding.patch'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..f88254bccf --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..54ded3244b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Created by Andrew Edmondson +# Copied from Automake-1.15-intel-2016b.eb, which had the following copywrite information: +# +# 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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..1fe6a834c7 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..31858dc8f2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..d16cac5f5d --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..36a239c230 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +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' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..65287edcc6 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Created by Andrew Edmondson . Copied from CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb, which had the following copywrite information: +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University, +# Forschungszentrum Juelich +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# Authors:: Damian Alvarez +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +#easyblock = 'ConfigureMake' + +name = 'CUDA' +version = '7.5.18' + +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': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] +checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] + +# Necessary to allow to use a GCC 4.9.3 toolchain, as CUDA by default just supports up to 4.9.2. +# Tested, but not throughly, so it is not guaranteed to don't cause problems +installopts = '-override compiler' + +host_compilers = ["icpc", "g++"] + +# Be careful and have a message consistent with the generated wrappers +modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" +modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created." + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..67f22b9f41 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.46.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..d5628e7fb3 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.11' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('CMake', '3.4.1'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..a74193a537 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..6a0888eaf0 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..e3d38f1976 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.16' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..04b53926ef --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..8730994eeb --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..2da711ec97 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +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/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..ab17db8531 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,34 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +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.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..9fa376ea1b --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..2d9153a9ad --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,35 @@ +name = 'netCDF' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.46.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.11'), + ('Szip', '2.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..e10bff0004 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..ed40bed006 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,137 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + #('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', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + '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', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + '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', '0.23.4', { + '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', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + '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/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + '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'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..6d4f59e1c2 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Created by Andrew Edmondson +# Copied from SQLite-3.9.2-intel-2016b.eb, which had the following copywrite information: +# +# 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 = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..30b6725636 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..b0142c9365 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..88cf038a76 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +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-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..28c7cc5e43 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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 74405a7c10c5a6e0c03b3c1b774f6af3e535c7b0 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Thu, 13 Oct 2016 15:57:06 +0100 Subject: [PATCH 162/350] 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 114fa5350b54e4793199f3680b4eb863815c8aed Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 13 Oct 2016 18:31:29 +0200 Subject: [PATCH 163/350] Fix conflicts --- easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb index 0e52dfb998..3f2d3b24f6 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb @@ -15,6 +15,6 @@ checksums = [ 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] -dependencies = [('M4', '1.4.17')] +dependencies = [('M4', '1.4.17', '', ('GNU', '4.9.3-2.25'))] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb index c1b7ac5006..cc528417f1 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb @@ -15,6 +15,6 @@ checksums = [ 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] -dependencies = [('M4', '1.4.17')] +dependencies = [('M4', '1.4.17', '', ('GNU', '4.9.3-2.25'))] moduleclass = 'lang' -- GitLab From 215efabdb5300d98116e159a077f99b8b7076d25 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 12:22:42 +0100 Subject: [PATCH 164/350] 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 165/350] {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 166/350] 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 1811b1522edc61071acafd4001a234d75f7ea11d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Oct 2016 13:33:20 +0200 Subject: [PATCH 167/350] {bio}[intel/2016b] RELION {1.4,2.0.1} (REVIEW) --- .../r/RELION/RELION-1.4-intel-2016b-single.eb | 32 +++++++++++++++++++ .../r/RELION/RELION-1.4-intel-2016b.eb | 31 ++++++++++++++++++ .../r/RELION/RELION-1.4_fltk-config.patch | 11 +++++++ .../r/RELION/RELION-2.0.1-intel-2016b.eb | 28 ++++++++++++++++ 4 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb create mode 100644 easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb create mode 100644 easybuild/easyconfigs/r/RELION/RELION-1.4_fltk-config.patch create mode 100644 easybuild/easyconfigs/r/RELION/RELION-2.0.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb new file mode 100644 index 0000000000..4af81b8528 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'RELION' +version = '1.4' +versionsuffix = '-single' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True} + +source_urls = ['http://www2.mrc-lmb.cam.ac.uk/groups/scheres/1sep15/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['RELION-%(version)s_fltk-config.patch'] + +dependencies = [ + ('X11', '20160819'), + ('FFTW', '3.3.5'), + ('FLTK', '1.3.3'), +] + +# RELION expects FLTK to be in external/fltk-1.3.0 and we have to add fltk libraries +configopts = '--enable-mpi --enable-float LIBS="-lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig ' +configopts += '-lXinerama -lpthread -lX11" && ln -s $EBROOTFLTK/include external/fltk-1.3.0 ' +# users expect the maingui binary to be called relion +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb new file mode 100644 index 0000000000..c159baafb4 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'RELION' +version = '1.4' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True} + +source_urls = ['http://www2.mrc-lmb.cam.ac.uk/groups/scheres/1sep15/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['RELION-%(version)s_fltk-config.patch'] + +dependencies = [ + ('X11', '20160819'), + ('FFTW', '3.3.5'), + ('FLTK', '1.3.3'), +] + +# RELION expects FLTK to be in external/fltk-1.3.0 and we have to add fltk libraries +configopts = '--enable-mpi LIBS="-lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig ' +configopts += '-lXinerama -lpthread -lX11" && ln -s $EBROOTFLTK/include external/fltk-1.3.0 ' +# users expect the maingui binary to be called relion +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.4_fltk-config.patch b/easybuild/easyconfigs/r/RELION/RELION-1.4_fltk-config.patch new file mode 100644 index 0000000000..22a822811f --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-1.4_fltk-config.patch @@ -0,0 +1,11 @@ +--- configure.orig 2014-08-11 17:18:31.686813247 +0200 ++++ configure 2014-08-11 17:18:39.390957858 +0200 +@@ -15846,7 +15846,7 @@ + #Check for FLTK + # as g++ seems needed and not gcc for compilation, + #just check for presence of fltk-config program +-fltkfile=`pwd`/bin/fltk-config ++fltkfile=`which fltk-config` + as_ac_File=`$as_echo "ac_cv_file_$fltkfile" | $as_tr_sh` + { $as_echo "$as_me:$LINENO: checking for $fltkfile" >&5 + $as_echo_n "checking for $fltkfile... " >&6; } diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.0.1-intel-2016b.eb b/easybuild/easyconfigs/r/RELION/RELION-2.0.1-intel-2016b.eb new file mode 100644 index 0000000000..2a14ff8652 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-2.0.1-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '2.0.1' +commit_id = 'a6225608e270' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True} + +source_urls = ['https://bitbucket.org/tcblab/relion2-beta/get/'] +sources = ['%s.tar.gz' % commit_id] + +builddependencies = [ + ('CMake', '3.6.2'), +] + +dependencies = [ + ('X11', '20160819'), + ('FFTW', '3.3.5'), + ('FLTK', '1.3.3'), +] + +moduleclass = 'bio' -- GitLab From b14ee7220da1bbc74379dc8da03d2b4e8e57ca11 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Oct 2016 14:03:06 +0200 Subject: [PATCH 168/350] {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 169/350] {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 170/350] 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 71b299142cf91dd55d1c6d8b4a7903dd6abfb398 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Thu, 13 Oct 2016 15:50:02 +0100 Subject: [PATCH 171/350] Amber 16 support for serial, MPI and CUDA builds - including all deps --- .../a/Amber/Amber-16-iomkl-2016.07-serial.eb | 32 ++++ .../a/Amber/Amber-16-iomkl-2016.07.eb | 32 ++++ ...er-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb | 32 ++++ ...oconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb | 26 ++++ ...omake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb | 36 +++++ ...s-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb | 17 +++ ...ison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb | 22 +++ ...zip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb | 15 ++ ...Make-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb | 31 ++++ ...5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 45 ++++++ ...URL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 31 ++++ ...gen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 19 +++ ...lex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb | 14 ++ .../GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 30 ++++ ...DF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb | 23 +++ ...adline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb | 32 ++++ ...tool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb | 17 +++ .../M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb | 23 +++ ...curses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 34 +++++ ...DF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb | 20 +++ ...tCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 35 +++++ ...SSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb | 19 +++ ...hon-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 137 ++++++++++++++++++ ...Lite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 43 ++++++ .../Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb | 23 +++ .../Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb | 25 ++++ .../Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb | 26 ++++ ...zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb | 22 +++ 28 files changed, 861 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb new file mode 100644 index 0000000000..35516d3232 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb @@ -0,0 +1,32 @@ +# +# Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +# +name = 'Amber' +version = '16' +ambertools_ver = '16' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (5, 14) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' %(ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'usempi': False} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] + +dependencies = [ + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +patches = ['Amber-16_fix-hardcoding.patch'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb new file mode 100644 index 0000000000..4551ed1bc9 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb @@ -0,0 +1,32 @@ +# +# Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +# +name = 'Amber' +version = '16' +ambertools_ver = '16' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (5, 14) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' %(ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'usempi': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] + +dependencies = [ + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +patches = ['Amber-16_fix-hardcoding.patch'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb new file mode 100644 index 0000000000..a2cab13af2 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb @@ -0,0 +1,32 @@ +# Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +# +name = 'Amber' +version = '16' +ambertools_ver = '16' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (5, 14) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' %(ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'usempi': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] + +dependencies = [ + ('CUDA', '7.5.18', '', ('iccifort', '2016.3.210-GCC-4.9.3-2.25')), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +patches = ['Amber-16_fix-hardcoding.patch'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..f88254bccf --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..54ded3244b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Created by Andrew Edmondson +# Copied from Automake-1.15-intel-2016b.eb, which had the following copywrite information: +# +# 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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..1fe6a834c7 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..31858dc8f2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..d16cac5f5d --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..36a239c230 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +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' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..65287edcc6 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Created by Andrew Edmondson . Copied from CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb, which had the following copywrite information: +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University, +# Forschungszentrum Juelich +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# Authors:: Damian Alvarez +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +#easyblock = 'ConfigureMake' + +name = 'CUDA' +version = '7.5.18' + +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': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} + +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux.run'] +checksums = ['4b3bcecf0dfc35928a0898793cf3e4c6'] + +# Necessary to allow to use a GCC 4.9.3 toolchain, as CUDA by default just supports up to 4.9.2. +# Tested, but not throughly, so it is not guaranteed to don't cause problems +installopts = '-override compiler' + +host_compilers = ["icpc", "g++"] + +# Be careful and have a message consistent with the generated wrappers +modloadmsg = "nvcc uses g++ as the default host compiler. If you want to use icpc as a host compiler you can use" +modloadmsg += " nvcc_icpc, or nvcc -ccbin=icpc. Likewise, a g++ wrapper called nvcc_g++ has been also created." + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..67f22b9f41 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.46.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..d5628e7fb3 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.11' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('CMake', '3.4.1'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..a74193a537 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..6a0888eaf0 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..e3d38f1976 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.16' + +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..04b53926ef --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.09-GCC-4.9.3-2.25.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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..8730994eeb --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..2da711ec97 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +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/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..ab17db8531 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,34 @@ +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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +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.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..9fa376ea1b --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..2d9153a9ad --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,35 @@ +name = 'netCDF' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.46.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.11'), + ('Szip', '2.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..e10bff0004 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.09-GCC-4.9.3-2.25.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': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..ed40bed006 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,137 @@ +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + #('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', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + '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', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + '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', '0.23.4', { + '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', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + '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/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + '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'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..6d4f59e1c2 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Created by Andrew Edmondson +# Copied from SQLite-3.9.2-intel-2016b.eb, which had the following copywrite information: +# +# 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 = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..30b6725636 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..b0142c9365 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..88cf038a76 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} + +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-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000..28c7cc5e43 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} +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 148e5e5b046f18991065df0e78b21dd9d7fbe825 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 15:39:39 +0100 Subject: [PATCH 172/350] Patch to reintroduce the test.cuda make target for backwards compatibility in the easyblock --- .../easyconfigs/a/Amber/Amber-16_test_cuda.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16_test_cuda.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16_test_cuda.patch b/easybuild/easyconfigs/a/Amber/Amber-16_test_cuda.patch new file mode 100644 index 0000000000..6b4af61766 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16_test_cuda.patch @@ -0,0 +1,13 @@ +--- Makefile.orig 2016-10-14 10:17:32.020437000 +0100 ++++ Makefile 2016-10-14 10:18:12.940992000 +0100 +@@ -80,6 +80,10 @@ + fi ;\ + ) + ++test.cuda: ++ # For backwards compatibility in the easyblock ++ -(cd test && $(MAKE) test.cuda.serial) ++ + test.cuda_serial: + -(cd test && $(MAKE) test.cuda.serial) + -- GitLab From 67b975991ded9262ebf146721256d9409a118826 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 15:43:14 +0100 Subject: [PATCH 173/350] Using patch in CUDA Amber build --- .../a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb index a2cab13af2..e8aeafd2cb 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb @@ -1,3 +1,6 @@ +# Automatically converted from Amber-16-iomkl-2016.09-CUDA.eb +# by /gpfs/sysapps/bham/scripts/easybuild/recursive_build_with_new_toolchain.py +# # Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb # name = 'Amber' @@ -27,6 +30,7 @@ dependencies = [ ('Python', '2.7.11'), ] -patches = ['Amber-16_fix-hardcoding.patch'] +patches = ['Amber-16_fix-hardcoding.patch', + 'Amber-16_test_cuda.patch'] moduleclass = 'chem' -- GitLab From fefc30ece55c4488acf1dbd16ff4318b5d1de346 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 15:52:30 +0100 Subject: [PATCH 174/350] Fixing bad filename --- ...25.eb => netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/n/netCDF-Fortran/{netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb => netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb} (100%) diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb similarity index 100% rename from easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-iomkl-2016.09-GCC-4.9.3-2.25.eb rename to easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb -- GitLab From 4fdd32e235b5e9ac4eb7305eb4b0d796ce1ac5d5 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 16:00:28 +0100 Subject: [PATCH 175/350] Renaming eb files to match expectations --- ...mber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb} | 0 ...eb => Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb} | 0 ...-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb} | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/Amber/{Amber-16-iomkl-2016.07-serial.eb => Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb} (100%) rename easybuild/easyconfigs/a/Amber/{Amber-16-iomkl-2016.07.eb => Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb} (100%) rename easybuild/easyconfigs/a/Amber/{Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb => Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb} (100%) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb similarity index 100% rename from easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-serial.eb rename to easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb similarity index 100% rename from easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07.eb rename to easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb similarity index 100% rename from easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-CUDA.eb rename to easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb -- GitLab From ec316941014552d91444a93c91ad3d650a817736 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 16:17:48 +0100 Subject: [PATCH 176/350] Adding missing patch file --- .../a/Amber/Amber-16_fix-hardcoding.patch | 117 ++++++++++++++++++ 1 file changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16_fix-hardcoding.patch b/easybuild/easyconfigs/a/Amber/Amber-16_fix-hardcoding.patch new file mode 100644 index 0000000000..a9b3ba5328 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16_fix-hardcoding.patch @@ -0,0 +1,117 @@ +diff -ur 16-iomkl-2016.09-patchlevel-14-5-serial/AmberTools/src/configure2 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src/configure2 +--- 16-iomkl-2016.09-patchlevel-14-5-serial/AmberTools/src/configure2 2016-10-06 14:27:01.000000000 +0100 ++++ 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src/configure2 2016-10-06 14:52:11.607328298 +0100 +@@ -513,6 +513,7 @@ + mpi='no' + mtkpp='install_mtkpp' + netcdf_dir='' ++netcdf_fort_dir='' + netcdf_flag='' + netcdfstatic='no' + pnetcdf_dir='' +@@ -587,6 +588,7 @@ + --skip-python) skippython='yes' ;; + --with-python) shift; python="$1";; + --with-netcdf) shift; netcdf_dir="$1";; ++ --with-netcdf-fort) shift; netcdf_fort_dir="$1";; + --with-pnetcdf) shift; pnetcdf_dir="$1" ;; + --python-install) shift; python_install="$1";; + -netcdfstatic) netcdfstatic='yes' ;; +@@ -778,7 +780,7 @@ + flibsf="-larpack -llapack -lblas" + # only used when the user requests a static build or when a static build is + # automatically set, eg, windows: +-staticflag='-static' ++staticflag='-static-intel' + omp_flag= + mpi_flag= + fp_flags= +@@ -1280,7 +1282,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1598,7 +1600,7 @@ + fi + + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$pmemd_coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1924,7 +1926,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2059,7 +2061,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2131,17 +2133,17 @@ + blas=skip + flibs="-larpack " + flibsf="-larpack " +- mkll="$MKL_HOME/lib/32" ++ mkll="$MKL_HOME/mkl/lib/32" + mkl_processor="32" + mkl_procstring="ia32" + mklinterfacelayer='libmkl_intel.a' + if [ "$x86_64" = 'yes' ]; then +- if [ -d "$MKL_HOME/lib/em64t" ]; then +- mkll="$MKL_HOME/lib/em64t" ++ if [ -d "$MKL_HOME/mkl/lib/em64t" ]; then ++ mkll="$MKL_HOME/mkl/lib/em64t" + mkl_processor="em64t" + mkl_procstring="em64t" + else +- mkll="$MKL_HOME/lib/intel64" ++ mkll="$MKL_HOME/mkl/lib/intel64" + mkl_processor="intel64" + mkl_procstring="intel64" + fi +@@ -2567,11 +2569,16 @@ + else + # A NetCDF directory was specified. Check that library exists and compiles + printf "\tUsing external NetCDF in '$netcdf_dir'\n" ++ # Support separate NetCDF-Fortran installation with --with-netcdf-fort ++ if [ ! -e "$netcdf_fort_dir" ]; then ++ netcdf_fort_dir="$netcdf_dir" ++ fi ++ printf "\tUsing external NetCDF-Fortran in '$netcdf_fort_dir'\n" + netcdfinc="-I"$netcdf_dir"/include" + if [ "${netcdf_dir}" != '/usr' -a "$netcdf_dir" != '/usr/' ]; then + netcdf_flag="-L${netcdf_dir}/lib $netcdf_flag" + fi +- netcdf=$netcdf_dir"/include/netcdf.mod" ++ netcdf=$netcdf_fort_dir"/include/netcdf.mod" + if [ "$netcdfstatic" = 'no' ] ; then + if [ "${netcdf_dir}" != '/usr' -a "${netcdf_dir}" != '/usr/' ]; then + netcdfflagc="-L${netcdf_dir}/lib -lnetcdf" +@@ -2587,7 +2594,7 @@ + echo "Error: '$netcdfflagc' not found." + exit 1 + fi +- netcdfflagf=$netcdf_dir"/lib/libnetcdff.a" ++ netcdfflagf=$netcdf_fort_dir"/lib/libnetcdff.a" + if [ ! -e "$netcdfflagf" ]; then + echo "Error: '$netcdfflagf' not found." + exit 1 +Only in 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src: configure2.orig +Only in 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src: configure2.rej +Only in 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src/cpptraj: configure.orig +Only in 16-iomkl-2016.09-patchlevel-14-5-serial.patched/AmberTools/src/cpptraj: configure.rej -- GitLab From 4e154140b38eacd6994b3f03cc43a9ab4b222961 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 16:28:19 +0100 Subject: [PATCH 177/350] Adding missing dependencies --- .../netCDF-Fortran-4.4.4-iomkl-2016.07.eb | 22 +++ .../n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb | 37 +++++ .../p/Python/Python-2.7.11-iomkl-2016.07.eb | 139 ++++++++++++++++++ 3 files changed, 198 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb new file mode 100644 index 0000000000..bd4b6d4d06 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb @@ -0,0 +1,22 @@ +# Automatically converted from netCDF-Fortran-4.4.3-foss-2015b.eb +# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.4.0')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb new file mode 100644 index 0000000000..95aa66e2a2 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb @@ -0,0 +1,37 @@ +# Automatically converted from netCDF-4.3.3.1-iomkl-2015.03.eb +# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py +name = 'netCDF' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.16'), + ('cURL', '7.46.0'), +] + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.11'), + ('Szip', '2.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb new file mode 100644 index 0000000000..c445811709 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb @@ -0,0 +1,139 @@ +# Automatically converted from Python-2.7.11-foss-2016.09.eb +# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py +name = 'Python' +version = '2.7.11' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.10.1' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.9.2'), + #('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', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '18.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + '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', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.1', { + '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', '0.23.4', { + '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', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.4', { + '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/'], + }), + ('paramiko', '1.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.6', { + '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'], + }), + ('funcsigs', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.2', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.3', { + # grab tarball from GitHub rather than PyPi since 3.1.3 release on PyPi disappeared; + # cfr. https://github.com/scott-griffiths/bitstring/issues/159 + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/scott-griffiths/bitstring/archive/'], + }), + ('virtualenv', '14.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' -- GitLab From a71eb2f3267fb22826a632c90ddca2a16cf8cc25 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Fri, 14 Oct 2016 16:57:12 +0100 Subject: [PATCH 178/350] Adding many more dependencies --- .../a/Autoconf/Autoconf-2.69-iomkl-2016.07.eb | 26 ++++++++++++ .../a/Automake/Automake-1.15-iomkl-2016.07.eb | 35 ++++++++++++++++ ...omake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- .../Autotools-20150215-iomkl-2016.07.eb | 17 ++++++++ .../b/Bison/Bison-3.0.4-iomkl-2016.07.eb | 22 ++++++++++ .../b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb | 15 +++++++ .../c/CMake/CMake-3.4.1-iomkl-2016.07.eb | 31 ++++++++++++++ ...5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- .../c/cURL/cURL-7.46.0-iomkl-2016.07.eb | 31 ++++++++++++++ .../d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb | 19 +++++++++ .../f/flex/flex-2.5.39-iomkl-2016.07.eb | 14 +++++++ .../g/GMP/GMP-6.1.0-iomkl-2016.07.eb | 30 +++++++++++++ .../h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb | 23 ++++++++++ .../libreadline-6.3-iomkl-2016.07.eb | 32 ++++++++++++++ .../l/libtool/libtool-2.4.6-iomkl-2016.07.eb | 17 ++++++++ .../m/M4/M4-1.4.17-iomkl-2016.07.eb | 23 ++++++++++ .../n/ncurses/ncurses-6.0-iomkl-2016.07.eb | 34 +++++++++++++++ .../netCDF-Fortran-4.4.4-iomkl-2016.07.eb | 2 - .../o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.07.eb | 19 +++++++++ .../s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb | 42 +++++++++++++++++++ ...Lite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- .../s/Szip/Szip-2.1-iomkl-2016.07.eb | 23 ++++++++++ .../t/Tcl/Tcl-8.6.4-iomkl-2016.07.eb | 25 +++++++++++ .../t/Tk/Tk-8.6.4-iomkl-2016.07.eb | 26 ++++++++++++ .../z/zlib/zlib-1.2.8-iomkl-2016.07.eb | 22 ++++++++++ 25 files changed, 529 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.07.eb new file mode 100644 index 0000000000..463a75eb42 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} + +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-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb new file mode 100644 index 0000000000..6ce681f7d9 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Created by Andrew Edmondson, copied from an original file with copyright: +# +# 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': 'iomkl', 'version': '2016.07'} + +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/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb index 54ded3244b..c23d974743 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -2,7 +2,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Created by Andrew Edmondson -# Copied from Automake-1.15-intel-2016b.eb, which had the following copywrite information: +# Copied from Automake-1.15-intel-2016b.eb, which had the following copyright information: # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.07.eb new file mode 100644 index 0000000000..d27dde01f2 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.07.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.07.eb new file mode 100644 index 0000000000..0027e83817 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-iomkl-2016.07.eb @@ -0,0 +1,22 @@ +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': 'iomkl', 'version': '2016.07'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb new file mode 100644 index 0000000000..6ad5b69ca6 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb new file mode 100644 index 0000000000..0204c038c7 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.4.1' + +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': 'iomkl', 'version': '2016.07'} + +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' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 65287edcc6..9c0bfae1a8 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Created by Andrew Edmondson . Copied from CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb, which had the following copywrite information: +# Created by Andrew Edmondson . Copied from CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb, which had the following copyright information: # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University, # Forschungszentrum Juelich diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb new file mode 100644 index 0000000000..4652a9953d --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.46.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb new file mode 100644 index 0000000000..869b0596c5 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb @@ -0,0 +1,19 @@ +name = 'Doxygen' +version = '1.8.11' + +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': 'iomkl', 'version': '2016.07'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('CMake', '3.4.1'), + ('Bison', '3.0.4'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.07.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.07.eb new file mode 100644 index 0000000000..06637a12c3 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.07.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.07.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.07.eb new file mode 100644 index 0000000000..e34edcb7af --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-iomkl-2016.07.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.0' + +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': 'iomkl', 'version': '2016.07'} +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/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb new file mode 100644 index 0000000000..d61bff1fff --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.16' + +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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.07.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.07.eb new file mode 100644 index 0000000000..8aff248e52 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} +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-iomkl-2016.07.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.07.eb new file mode 100644 index 0000000000..436ada208a --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.07.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.07.eb new file mode 100644 index 0000000000..b6bbaa91c0 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} + +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/n/ncurses/ncurses-6.0-iomkl-2016.07.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb new file mode 100644 index 0000000000..77201153ed --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb @@ -0,0 +1,34 @@ +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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +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.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb index bd4b6d4d06..8745f48528 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb @@ -1,5 +1,3 @@ -# Automatically converted from netCDF-Fortran-4.4.3-foss-2015b.eb -# by /gpfs/sysapps/bham/scripts/easybuild/copy_to_toolchain.py name = 'netCDF-Fortran' version = '4.4.4' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.07.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.07.eb new file mode 100644 index 0000000000..89d8603d59 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} +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/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb new file mode 100644 index 0000000000..620b2e4dcc --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Created by Andrew Edmondson, copied from an original file with copyright: +# +# 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 = '3.9.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'iomkl', 'version': '2016.07'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb index 6d4f59e1c2..c4174cdb80 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -2,7 +2,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Created by Andrew Edmondson -# Copied from SQLite-3.9.2-intel-2016b.eb, which had the following copywrite information: +# Copied from SQLite-3.9.2-intel-2016b.eb, which had the following copyright information: # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb new file mode 100644 index 0000000000..85c164d4c0 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.07.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.07.eb new file mode 100644 index 0000000000..598c79f35a --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-iomkl-2016.07.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb new file mode 100644 index 0000000000..a5d63e7d00 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} + +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-iomkl-2016.07.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.eb new file mode 100644 index 0000000000..2242559968 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.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': 'iomkl', 'version': '2016.07'} +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 3ba9d7de5af972cfb8b938c74c3f337e8b8b3f37 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 17 Oct 2016 10:13:11 +0200 Subject: [PATCH 179/350] LIBS in one line --- .../easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb | 5 +++-- easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb index 4af81b8528..add5ffc72c 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb @@ -24,8 +24,9 @@ dependencies = [ ] # RELION expects FLTK to be in external/fltk-1.3.0 and we have to add fltk libraries -configopts = '--enable-mpi --enable-float LIBS="-lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig ' -configopts += '-lXinerama -lpthread -lX11" && ln -s $EBROOTFLTK/include external/fltk-1.3.0 ' +configopts = '--enable-mpi --enable-float ' +configopts += 'LIBS="-lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig -lXinerama -lpthread -lX11" ' +configopts += '&& ln -s $EBROOTFLTK/include external/fltk-1.3.0 ' # users expect the maingui binary to be called relion installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb index c159baafb4..74acae10a1 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b.eb @@ -23,8 +23,9 @@ dependencies = [ ] # RELION expects FLTK to be in external/fltk-1.3.0 and we have to add fltk libraries -configopts = '--enable-mpi LIBS="-lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig ' -configopts += '-lXinerama -lpthread -lX11" && ln -s $EBROOTFLTK/include external/fltk-1.3.0 ' +configopts = '--enable-mpi ' +configopts += 'LIBS="-lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig -lXinerama -lpthread -lX11" ' +configopts += '&& ln -s $EBROOTFLTK/include external/fltk-1.3.0 ' # users expect the maingui binary to be called relion installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " -- GitLab From 056fd4508ad7fd00655928fc0b5ca8584f32d6de Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Mon, 17 Oct 2016 09:18:56 +0100 Subject: [PATCH 180/350] Removing header modifications where only the toolchain has been changed --- .../easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb | 2 -- .../a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb | 3 --- .../c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 -- easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb | 2 -- .../s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 3 --- 5 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb index 6ce681f7d9..d787cbd50b 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb @@ -1,8 +1,6 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Created by Andrew Edmondson, copied from an original file with copyright: -# # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb index c23d974743..c8260533e6 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -1,9 +1,6 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Created by Andrew Edmondson -# Copied from Automake-1.15-intel-2016b.eb, which had the following copyright information: -# # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 9c0bfae1a8..8ed8a29bfc 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,8 +1,6 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Created by Andrew Edmondson . Copied from CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb, which had the following copyright information: -# # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University, # Forschungszentrum Juelich # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb index 620b2e4dcc..4eb223b17f 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb @@ -1,8 +1,6 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Created by Andrew Edmondson, copied from an original file with copyright: -# # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb index c4174cdb80..e099c4dd67 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -1,9 +1,6 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Created by Andrew Edmondson -# Copied from SQLite-3.9.2-intel-2016b.eb, which had the following copyright information: -# # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL -- GitLab From 95b29a4626a0b264462bd78571318d1a4d86447a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2016 10:20:57 +0200 Subject: [PATCH 181/350] 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 997867d45cd4ae73b396a3b6a8e8e4a581e70c5c Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Mon, 17 Oct 2016 10:55:42 +0100 Subject: [PATCH 182/350] PR review comments from https://github.com/hpcugent/easybuild-easyconfigs/pull/3688#pullrequestreview-4430366 --- ...2016.07-AmberTools-16-patchlevel-5-14-serial.eb | 7 ++----- ...-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb | 7 ++----- ....9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb | 14 +++++--------- .../c/cURL/cURL-7.46.0-iomkl-2016.07.eb | 2 +- .../cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- .../d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb | 2 +- .../Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- ...omkl-2016.07.eb => flex-2.6.0-iomkl-2016.07.eb} | 5 ++++- ... => flex-2.6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb} | 5 ++++- .../netCDF-Fortran-4.4.4-iomkl-2016.07.eb | 7 ++----- ...F-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb | 7 ++----- .../n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb | 7 ++----- .../netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 7 ++----- .../easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb | 2 +- .../easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb | 2 +- .../t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.eb | 2 +- .../zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- 18 files changed, 34 insertions(+), 50 deletions(-) rename easybuild/easyconfigs/f/flex/{flex-2.5.39-iomkl-2016.07.eb => flex-2.6.0-iomkl-2016.07.eb} (82%) rename easybuild/easyconfigs/f/flex/{flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb => flex-2.6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb} (82%) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb index 35516d3232..4e451954c3 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb @@ -1,6 +1,3 @@ -# -# Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb -# name = 'Amber' version = '16' ambertools_ver = '16' @@ -21,12 +18,12 @@ sources = [ 'AmberTools%s.tar.bz2' % ambertools_ver, ] +patches = ['Amber-%(version)s_fix-hardcoding.patch'] + dependencies = [ ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), ] -patches = ['Amber-16_fix-hardcoding.patch'] - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb index 4551ed1bc9..f910ba5400 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb @@ -1,6 +1,3 @@ -# -# Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb -# name = 'Amber' version = '16' ambertools_ver = '16' @@ -21,12 +18,12 @@ sources = [ 'AmberTools%s.tar.bz2' % ambertools_ver, ] +patches = ['Amber-%(version)s_fix-hardcoding.patch'] + dependencies = [ ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), ] -patches = ['Amber-16_fix-hardcoding.patch'] - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb index e8aeafd2cb..1b29f57d52 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb @@ -1,8 +1,3 @@ -# Automatically converted from Amber-16-iomkl-2016.09-CUDA.eb -# by /gpfs/sysapps/bham/scripts/easybuild/recursive_build_with_new_toolchain.py -# -# Based on https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb -# name = 'Amber' version = '16' ambertools_ver = '16' @@ -23,14 +18,15 @@ sources = [ 'AmberTools%s.tar.bz2' % ambertools_ver, ] +patches = ['Amber-%(version)s_fix-hardcoding.patch', + 'Amber-%(version)s_test_cuda.patch'] + + dependencies = [ - ('CUDA', '7.5.18', '', ('iccifort', '2016.3.210-GCC-4.9.3-2.25')), + ('CUDA', '7.5.18', '', True), ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), ] -patches = ['Amber-16_fix-hardcoding.patch', - 'Amber-16_test_cuda.patch'] - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb index 4652a9953d..85d8a32448 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.07.eb @@ -24,7 +24,7 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} sanity_check_paths = { - 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb index 67f22b9f41..fa8f0b1dc2 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.46.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -24,7 +24,7 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} sanity_check_paths = { - 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb index 869b0596c5..2cfa765309 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.07.eb @@ -11,7 +11,7 @@ sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] builddependencies = [ - ('flex', '2.5.39'), + ('flex', '2.6.0'), ('CMake', '3.4.1'), ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb index d5628e7fb3..215719decb 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -11,7 +11,7 @@ sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] builddependencies = [ - ('flex', '2.5.39'), + ('flex', '2.6.0'), ('CMake', '3.4.1'), ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.07.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.07.eb similarity index 82% rename from easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.07.eb rename to easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.07.eb index 06637a12c3..783366f34a 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.07.eb @@ -1,5 +1,5 @@ name = 'flex' -version = '2.5.39' +version = '2.6.0' homepage = 'http://flex.sourceforge.net/' description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, @@ -11,4 +11,7 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb similarity index 82% rename from easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb rename to easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb index a74193a537..a3d444f9de 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ name = 'flex' -version = '2.5.39' +version = '2.6.0' homepage = 'http://flex.sourceforge.net/' description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, @@ -11,4 +11,7 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +dependencies = [('M4', '1.4.17')] +builddependencies = [('Bison', '3.0.4')] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb index 8745f48528..0706679ca3 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.07.eb @@ -9,11 +9,8 @@ description = """NetCDF (network Common Data Form) is a set of software librarie toolchain = {'name': 'iomkl', 'version': '2016.07'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', - 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', -] +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive'] dependencies = [('netCDF', '4.4.0')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb index 9fa376ea1b..9dd4898f43 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -9,11 +9,8 @@ description = """NetCDF (network Common Data Form) is a set of software librarie toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', - 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', -] +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive'] dependencies = [('netCDF', '4.4.0')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb index 95aa66e2a2..a0a822a673 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb @@ -11,11 +11,8 @@ description = """NetCDF (network Common Data Form) is a set of software librarie toolchain = {'name': 'iomkl', 'version': '2016.07'} toolchainopts = {'pic': True, 'usempi': True} -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', - 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', -] +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] dependencies = [ ('HDF5', '1.8.16'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb index 2d9153a9ad..eec48bea4a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -9,11 +9,8 @@ description = """NetCDF (network Common Data Form) is a set of software librarie toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} toolchainopts = {'pic': True, 'usempi': True} -sources = [SOURCELOWER_TAR_GZ] -source_urls = [ - 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', - 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', -] +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] dependencies = [ ('HDF5', '1.8.16'), diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb index 85c164d4c0..512dbbe733 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.so"] + + 'files': ["lib/libsz.a", "lib/libsz.%s" %SHLIB_EXT] + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], 'dirs': [], } diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb index a5d63e7d00..f75495a398 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iomkl', 'version': '2016.07'} 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'] +patches = ['Tk-%(version)ss_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb index 88cf038a76..6e7e7c9ce9 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} 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'] +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.eb index 2242559968..5afd211f68 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.07.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': [], } diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb index 28c7cc5e43..66cf47a99c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iomkl-2016.09-GCC-4.9.3-2.25.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 ffd90cc8bd7169b898de38ae981b503d1f4abba2 Mon Sep 17 00:00:00 2001 From: Andrew Edmondson Date: Mon, 17 Oct 2016 11:39:45 +0100 Subject: [PATCH 183/350] Spurious s in format string --- easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb index f75495a398..fb10fedcae 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-iomkl-2016.07.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iomkl', 'version': '2016.07'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -patches = ['Tk-%(version)ss_different-prefix-with-tcl.patch'] +patches = ['Tk-%(version)s_different-prefix-with-tcl.patch'] dependencies = [ ('Tcl', version), -- GitLab From bed9d654f559b6b7e5e6d43ccf990fcab31e59de Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 17 Oct 2016 15:00:12 +0200 Subject: [PATCH 184/350] 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 185/350] 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 186/350] 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 187/350] {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 188/350] 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 189/350] 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 190/350] 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 e061a8e98690ee0af232707b7441b177e99d17b7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 22 Oct 2016 19:49:18 +0200 Subject: [PATCH 191/350] Make OpenBLAS use the LAPACK version specified in the easyconfig. The OpenBLAS Makefile only handles large.tgz and timing.tgz and ignores lapack-x.y.z.tgz. We need to manually unpack the lapack-x.y.z specified in the easyconfig. Doing it this way makse it possible to add patches on top of the unpacked lapack version, which is neccesary to deal with various compiler problems. --- .../OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 5 +++-- .../o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb | 5 +++-- .../o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb | 5 +++-- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb index 3183ffeabd..257f234cab 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -3,6 +3,8 @@ easyblock = 'ConfigureMake' name = 'OpenBLAS' version = '0.2.18' +obv = '%s-%s' % (name, version) # To be used in the lapack-x.y.z unpack cmd + lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver @@ -16,7 +18,7 @@ large_src = 'large.tgz' timing_src = 'timing.tgz' sources = [ 'v%(version)s.tar.gz', - lapack_src, + (lapack_src, 'mv %s/lapack-netlib %s/lapack-netlib.old; mkdir %s/lapack-netlib; tar -C %s/lapack-netlib --strip-components=1 -zxf %%s' % (obv, obv, obv, obv)), large_src, timing_src, ] @@ -28,7 +30,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] 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 index 75a0bc06f7..19e70c7dbd 100644 --- 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 @@ -3,6 +3,8 @@ easyblock = 'ConfigureMake' name = 'OpenBLAS' version = '0.2.18' +obv = '%s-%s' % (name, version) # To be used in the lapack-x.y.z unpack cmd + lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver @@ -16,7 +18,7 @@ large_src = 'large.tgz' timing_src = 'timing.tgz' sources = [ 'v%(version)s.tar.gz', - lapack_src, + (lapack_src, 'mv %s/lapack-netlib %s/lapack-netlib.old; mkdir %s/lapack-netlib; tar -C %s/lapack-netlib --strip-components=1 -zxf %%s' % (obv, obv, obv, obv)), large_src, timing_src, ] @@ -28,7 +30,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] 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 index 32b66ddad1..7145750599 100644 --- 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 @@ -3,6 +3,8 @@ easyblock = 'ConfigureMake' name = 'OpenBLAS' version = '0.2.19' +obv = '%s-%s' % (name, version) # To be used in the lapack-x.y.z unpack cmd + lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver @@ -16,7 +18,7 @@ large_src = 'large.tgz' timing_src = 'timing.tgz' sources = [ 'v%(version)s.tar.gz', - lapack_src, + (lapack_src, 'mv %s/lapack-netlib %s/lapack-netlib.old; mkdir %s/lapack-netlib; tar -C %s/lapack-netlib --strip-components=1 -zxf %%s' % (obv, obv, obv, obv)), large_src, timing_src, ] @@ -28,7 +30,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] -- GitLab From b4749bb569a4da28304a1914a6ac1a591f671a21 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 24 Oct 2016 09:33:06 +0200 Subject: [PATCH 192/350] Change the lapack-x.y.z.tgz unpacking to a more readable version. Also don't keep a copy of the old lapack-netlib. --- .../OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 9 ++++++--- .../OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb | 9 ++++++--- .../OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb | 9 ++++++--- 3 files changed, 18 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb index 257f234cab..eb1d2f67c9 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -3,8 +3,6 @@ easyblock = 'ConfigureMake' name = 'OpenBLAS' version = '0.2.18' -obv = '%s-%s' % (name, version) # To be used in the lapack-x.y.z unpack cmd - lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver @@ -16,9 +14,14 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %s-%s; rm -rf lapack-netlib;' % (name, version) +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + sources = [ 'v%(version)s.tar.gz', - (lapack_src, 'mv %s/lapack-netlib %s/lapack-netlib.old; mkdir %s/lapack-netlib; tar -C %s/lapack-netlib --strip-components=1 -zxf %%s' % (obv, obv, obv, obv)), + (lapack_src, lapack_unpack_cmd), large_src, timing_src, ] 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 index 19e70c7dbd..35ba0998f3 100644 --- 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 @@ -3,8 +3,6 @@ easyblock = 'ConfigureMake' name = 'OpenBLAS' version = '0.2.18' -obv = '%s-%s' % (name, version) # To be used in the lapack-x.y.z unpack cmd - lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver @@ -16,9 +14,14 @@ toolchain = {'name': 'gompi', 'version': '2016.07'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %s-%s; rm -rf lapack-netlib;' % (name, version) +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + sources = [ 'v%(version)s.tar.gz', - (lapack_src, 'mv %s/lapack-netlib %s/lapack-netlib.old; mkdir %s/lapack-netlib; tar -C %s/lapack-netlib --strip-components=1 -zxf %%s' % (obv, obv, obv, obv)), + (lapack_src, lapack_unpack_cmd), large_src, timing_src, ] 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 index 7145750599..0755e77fbc 100644 --- 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 @@ -3,8 +3,6 @@ easyblock = 'ConfigureMake' name = 'OpenBLAS' version = '0.2.19' -obv = '%s-%s' % (name, version) # To be used in the lapack-x.y.z unpack cmd - lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver @@ -16,9 +14,14 @@ toolchain = {'name': 'gompi', 'version': '2016.09'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %s-%s; rm -rf lapack-netlib;' % (name, version) +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + sources = [ 'v%(version)s.tar.gz', - (lapack_src, 'mv %s/lapack-netlib %s/lapack-netlib.old; mkdir %s/lapack-netlib; tar -C %s/lapack-netlib --strip-components=1 -zxf %%s' % (obv, obv, obv, obv)), + (lapack_src, lapack_unpack_cmd), large_src, timing_src, ] -- GitLab From 8335ca81fdd984b961935d564c5cf2ee8de62e49 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 24 Oct 2016 10:21:15 +0200 Subject: [PATCH 193/350] 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 194/350] 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 2998ebf873a9ee1de07f3fb872fd122b5b65fbdb Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Mon, 24 Oct 2016 18:03:16 +0200 Subject: [PATCH 195/350] Update WRF-3.8.0_netCDF-Fortran_separate_path.patch I believe this is a typo preventing the `NETCDFFPATH` variable to be set correctly. --- .../w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch index f46ae78e87..baaf9b3859 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0_netCDF-Fortran_separate_path.patch @@ -83,7 +83,7 @@ diff -ru WRFV3.orig/arch/postamble_new WRFV3/arch/postamble_new ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE NETCDFPATH = CONFIGURE_NETCDF_PATH -++NETCDFFPATH = CONFIGURE_NETCDFF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH HDF5PATH = CONFIGURE_HDF5_PATH WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH PNETCDFPATH = CONFIGURE_PNETCDF_PATH -- GitLab From 3896361f1544a31dc8701a1f564c1bda7d86cb32 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2016 12:25:08 +0200 Subject: [PATCH 196/350] add custom patch for OpenFOAM 3.0.1 --- .../o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb | 2 +- .../o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch | 282 ++++++++++++++++++ 2 files changed, 283 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb index ca5d08b992..e27c7e7895 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb @@ -15,7 +15,7 @@ sources = ['version-%(version)s.tar.gz'] checksums = ['a6ffe3edabdd23f9eff31be47a092b07'] -patches = ['OpenFOAM-3.0.0_cleanup.patch'] +patches = ['OpenFOAM-%(version)s_cleanup.patch'] dependencies = [ ('libreadline', '6.3'), diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch new file mode 100644 index 0000000000..335b44903b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch @@ -0,0 +1,282 @@ +# 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 , Kenneth Hoste +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-3.0.x-version-3.0.1/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/mesh/manipulation/setSet/Allwmake 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-10-25 11:51:45.000000000 +0200 +@@ -6,11 +6,11 @@ + # + # 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$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/postProcessing/graphics/PV3Readers/Allwmake OpenFOAM-3.0.x-version-3.0.1/applications/utilities/postProcessing/graphics/PV3Readers/Allwmake +--- OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/postProcessing/graphics/PV3Readers/Allwmake 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/applications/utilities/postProcessing/graphics/PV3Readers/Allwmake 2016-10-25 12:00:41.000000000 +0200 +@@ -12,7 +12,7 @@ + } + + # ensure CMake gets the correct C++ compiler +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake libso vtkPV3Readers + PV3blockMeshReader/Allwmake +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/postProcessing/graphics/PV4Readers/Allwmake OpenFOAM-3.0.x-version-3.0.1/applications/utilities/postProcessing/graphics/PV4Readers/Allwmake +--- OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/postProcessing/graphics/PV4Readers/Allwmake 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/applications/utilities/postProcessing/graphics/PV4Readers/Allwmake 2016-10-25 12:00:41.000000000 +0200 +@@ -12,7 +12,7 @@ + } + + # ensure CMake gets the correct C++ compiler +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake libso vtkPV4Readers + PV4blockMeshReader/Allwmake +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/CGAL.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/CGAL.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/CGAL.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/CGAL.sh 2016-10-25 12:04:22.000000000 +0200 +@@ -29,29 +29,5 @@ + # Sourced from OpenFOAM-/etc/bashrc + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=CGAL-4.7 +- +-export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$boost_version +-export CGAL_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cgal_version +- +-if [ "$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" ] +-then +- _foamAddLib $CGAL_ARCH_PATH/lib +-fi +- +-if [ -d "$BOOST_ARCH_PATH" ] +-then +- _foamAddLib $BOOST_ARCH_PATH/lib +-fi +- +-unset boost_version cgal_version +- +-# ----------------------------------------------------------------------------- ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/gperftools.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/gperftools.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/gperftools.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/gperftools.sh 2016-10-25 12:05:33.000000000 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$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:$LD_LIBRARY_PATH ++PERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/metis.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/metis.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/metis.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/metis.sh 2016-10-25 12:06:03.000000000 +0200 +@@ -33,7 +33,7 @@ + # during the wmake process + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/paraview.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/paraview.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/paraview.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/paraview.sh 2016-10-25 12:09:26.000000000 +0200 +@@ -36,29 +36,16 @@ + # clean the PATH + cleaned=`$WM_PROJECT_DIR/bin/foamCleanPath "$PATH" "$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/cmake- $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/paraview-"` && PATH="$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 PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 + #export ParaView_VERSION=4.0.1 + #export ParaView_VERSION=4.1.0 + #export ParaView_VERSION=4.3.1 +-export ParaView_VERSION=4.4.0 ++#export ParaView_VERSION=4.4.0 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + +- + # Evaluate command-line parameters for ParaView + _foamParaviewEval() + { +@@ -95,16 +82,12 @@ + paraviewInstDir=$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 $ParaView_DIR/include/paraview ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + if [ ! -d $ParaView_LIB_DIR -a -d $ParaView_DIR/lib/paraview ] +@@ -112,8 +95,6 @@ + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview + fi + +- 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" ] +@@ -125,17 +106,6 @@ + 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:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/scotch.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/scotch.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/scotch.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/scotch.sh 2016-10-25 12:12:06.000000000 +0200 +@@ -33,7 +33,7 @@ + # during the wmake process + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/settings.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/settings.sh +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/settings.sh 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/config/settings.sh 2016-10-25 12:13:20.000000000 +0200 +@@ -87,11 +87,11 @@ + 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' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$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"\ +@@ -598,6 +598,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/ptscotchDecomp/Make/options 2016-10-25 12:13:37.000000000 +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 -ru OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-10-25 12:13:37.000000000 +0200 +@@ -119,10 +119,11 @@ + #include "globalIndex.H" + #include "SubField.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-3.0.x-version-3.0.1.orig/src/parallel/decompose/scotchDecomp/Make/options 2015-12-15 12:20:08.000000000 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/src/parallel/decompose/scotchDecomp/Make/options 2016-10-25 12:13:37.000000000 +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 0f98864cd461e2d8e5df95458ac2db8f9f18c227 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2016 12:56:15 +0200 Subject: [PATCH 197/350] 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 198/350] 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 199/350] {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 200/350] {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 201/350] {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 202/350] {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 203/350] {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 204/350] {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 205/350] {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 206/350] {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 207/350] {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 208/350] {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 209/350] {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 9a96eef5acf5432b5085447ba6d5e6384d1fb237 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 25 Oct 2016 15:29:32 +0200 Subject: [PATCH 210/350] {math}[intel/2016b] Octave 4.0.3 (REVIEW) --- .../o/Octave/Octave-4.0.3-intel-2016b.eb | 59 +++++++++++++++++++ .../o/Octave/Octave-4.0.3_intel.patch | 35 +++++++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.0.3_intel.patch diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb new file mode 100644 index 0000000000..804ee42715 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.0.3' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_intel.patch'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('X11', '20160819'), + ('PCRE', '8.39'), + ('ncurses', '6.0'), + ('libreadline', '6.3'), + ('arpack-ng', '3.4.0'), + ('cURL', '7.49.1'), + ('FLTK', '1.3.3'), + ('fontconfig', '2.12.1'), + ('freetype', '2.6.5'), + ('GLPK', '4.60'), + ('GL2PS', '1.3.9'), + ('gnuplot', '5.0.5'), + ('Java', '1.8.0_112', '', True), + ('zlib', '1.2.8'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt', '4.8.7'), + ('HDF5', '1.8.17', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.3', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.25'), + ('FFTW', '3.3.5'), +] + +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-4.0.3_intel.patch new file mode 100644 index 0000000000..71297e00cf --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3_intel.patch @@ -0,0 +1,35 @@ +Intel compiler does not understand __builtin_*_overflow +# Oct 25th 2016 by B. Hajgato (Free University Brussels - VUB) +--- octave-4.0.3/libgnu/xalloc-oversized.h.orig 2016-07-01 20:43:46.000000000 +0200 ++++ octave-4.0.3/libgnu/xalloc-oversized.h 2016-10-24 16:05:11.093643937 +0200 +@@ -36,7 +36,7 @@ + sizeof (ptrdiff_t) <= sizeof (size_t), so do not bother to test for + exactly-SIZE_MAX allocations on such hosts; this avoids a test and + branch when S is known to be 1. */ +-#if 5 <= __GNUC__ || __has_builtin (__builtin_mul_overflow) ++#if ((5 <= __GNUC__ || __has_builtin (__builtin_mul_overflow)) && !__INTEL_COMPILER) + # define xalloc_oversized(n, s) \ + ({ size_t __xalloc_size; __builtin_mul_overflow (n, s, &__xalloc_size); }) + #else +--- octave-4.0.3/libgnu/glob.c.orig 2016-10-24 16:11:56.437441986 +0200 ++++ octave-4.0.3/libgnu/glob.c 2016-10-24 16:12:21.127612656 +0200 +@@ -257,7 +257,7 @@ + static bool + size_add_wrapv (size_t a, size_t b, size_t *r) + { +-#if 5 <= __GNUC__ || __has_builtin (__builtin_add_overflow) ++#if ((5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) && !__INTEL_COMPILER) + return __builtin_add_overflow (a, b, r); + #else + *r = a + b; +--- octave-4.0.3/libgnu/intprops.h.orig 2016-07-01 20:43:43.000000000 +0200 ++++ octave-4.0.3/libgnu/intprops.h 2016-10-24 16:23:43.652325264 +0200 +@@ -353,7 +353,7 @@ + /* Store A B into *R, where OP specifies the operation. + BUILTIN is the builtin operation, and OVERFLOW the overflow predicate. + See above for restrictions. */ +-#if 5 <= __GNUC__ || __has_builtin (__builtin_add_overflow) ++#if ((5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) && !__INTEL_COMPILER) + # define _GL_INT_OP_WRAPV(a, b, r, op, builtin, overflow) builtin (a, b, r) + #elif 201112 <= __STDC_VERSION__ && !_GL__GENERIC_BOGUS + # define _GL_INT_OP_WRAPV(a, b, r, op, builtin, overflow) \ -- GitLab From 007e3efccda1f85195c00a3d70a5edba2ed5d288 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Oct 2016 15:55:15 +0200 Subject: [PATCH 211/350] 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 212/350] 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 213/350] 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 214/350] 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 215/350] 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 216/350] 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__}/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 0 .../{ => __archive__}/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 0 .../q/QLogicMPI/QLogicMPI-2.9-926.1005_rhel5_qlc.eb | 0 .../s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb | 0 ...aLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb | 0 .../ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb | 0 .../easyconfigs/{ => __archive__}/s/Szip/Szip-2.1-iqacml-3.7.3.eb | 0 .../{ => __archive__}/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb | 0 .../{ => __archive__}/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb | 0 .../{ => __archive__}/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb | 0 .../{ => __archive__}/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb | 0 .../{ => __archive__}/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb | 0 .../{ => __archive__}/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb | 0 52 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/b/BLACS/BLACS-1.1-iiqmpi-3.3.0.eb (100%) rename easybuild/easyconfigs/{ => 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(100%) rename easybuild/easyconfigs/{ => __archive__}/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/Szip/Szip-2.1-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb (100%) diff --git a/easybuild/easyconfigs/b/BLACS/BLACS-1.1-iiqmpi-3.3.0.eb b/easybuild/easyconfigs/__archive__/b/BLACS/BLACS-1.1-iiqmpi-3.3.0.eb similarity index 100% rename from easybuild/easyconfigs/b/BLACS/BLACS-1.1-iiqmpi-3.3.0.eb rename to 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diff --git a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/c/CBLAS/CBLAS-20110120-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/c/CBLAS/CBLAS-20110120-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.28.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/c/cURL/cURL-7.28.1-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/c/cURL/cURL-7.28.1-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/c/cURL/cURL-7.28.1-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-6.1.1-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/e/ESMF/ESMF-6.1.1-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iiqmpi-3.3.0.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-iiqmpi-3.3.0.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iiqmpi-3.3.0.eb rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-iiqmpi-3.3.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iiqmpi-4.4.13.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-iiqmpi-4.4.13.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-iiqmpi-4.4.13.eb rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-iiqmpi-4.4.13.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.35-iqacml-3.7.3.eb 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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 217/350] 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 218/350] 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 219/350] 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 220/350] 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 b/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.0.2-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/b/Bison/Bison-3.0.2-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.4-gpsmpi-2014.12.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb 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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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 222/350] 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 223/350] 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 rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb similarity index 100% rename from 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 224/350] 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 (100%) rename easybuild/easyconfigs/{ => __archive__}/g/goolf/goolf-1.5.14-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/i/IMB/IMB-4.0.1-goolf-1.5.14-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libffi/libffi-3.0.13-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-no-OFED-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-no-OFED-LAPACK-3.5.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/PAPI/PAPI-5.2.0-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/Scalasca/Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb (100%) rename 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easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.10.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.10.2-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/c/CMake/CMake-2.8.10.2-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/c/CMake/CMake-2.8.10.2-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb 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a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb rename to 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easybuild/easyconfigs/g/gettext/gettext-0.18.2-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.4.10-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/gompi/gompi-1.4.10-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/gompi/gompi-1.4.10-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/gompi/gompi-1.4.10-no-OFED.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/gompi/gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/gompi/gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/gompi/gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.5.14-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/gompi/gompi-1.5.14-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/gompi/gompi-1.5.14-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/gompi/gompi-1.5.14-no-OFED.eb diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/goolf/goolf-1.4.10-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/goolf/goolf-1.4.10-no-OFED.eb diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/goolf/goolf-1.5.14-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/goolf/goolf-1.5.14-no-OFED.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb diff 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a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libffi/libffi-3.0.13-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-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 225/350] 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 226/350] move easyconfigs for deprecated gmvolf toolchains to archive --- .../{ => __archive__}/b/BLACS/BLACS-1.1-gmvapich2-1.6.7.eb | 0 .../{ => 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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 227/350] 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 228/350] 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 229/350] 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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__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%) 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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 230/350] 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 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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 231/350] 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 232/350] 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 233/350] 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 234/350] 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 235/350] 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 236/350] 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 237/350] 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 238/350] 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 From 81f523425d799dccef415bb82bbd00b59583ff73 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 31 Oct 2016 10:43:12 +0100 Subject: [PATCH 239/350] Qt/moc problems solution try 1 --- easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb index 804ee42715..41dae6b7a6 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb @@ -47,7 +47,11 @@ dependencies = [ ('FFTW', '3.3.5'), ] -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' +configopts = 'MOC=$EBROOTQT/bin/moc ' +configopts += 'UIC=$EBROOTQT/bin/uic ' +configopts += 'RCC=$EBROOTQT/bin/rcc +configopts += 'LRELEASE=$EBROOTQT/bin/lrelease ' +configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' sanity_check_paths = { 'files': ['bin/octave'], -- GitLab From 6fbf212988e9ce0373bd024e5eae9384b68d0e00 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 31 Oct 2016 10:47:23 +0100 Subject: [PATCH 240/350] Qt/moc problem solution try 1 --- easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb index e136d733e5..2c1083acb3 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -46,7 +46,11 @@ dependencies = [ ('GraphicsMagick', '1.3.23'), ] -configopts = 'MOC=$EBROOTQT/bin/moc --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +configopts = 'MOC=$EBROOTQT/bin/moc ' +configopts += 'UIC=$EBROOTQT/bin/uic ' +configopts += 'RCC=$EBROOTQT/bin/rcc +configopts += 'LRELEASE=$EBROOTQT/bin/lrelease ' +configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' sanity_check_paths = { 'files': ['bin/octave'], -- GitLab From 5cf961fedd00f5bf5baef5150e8b218f1777a7d3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 31 Oct 2016 10:54:45 +0100 Subject: [PATCH 241/350] missing ' added --- easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb index 2c1083acb3..4d50479b08 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -48,7 +48,7 @@ dependencies = [ configopts = 'MOC=$EBROOTQT/bin/moc ' configopts += 'UIC=$EBROOTQT/bin/uic ' -configopts += 'RCC=$EBROOTQT/bin/rcc +configopts += 'RCC=$EBROOTQT/bin/rcc ' configopts += 'LRELEASE=$EBROOTQT/bin/lrelease ' configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' -- GitLab From 5d88e60bd3851d95d60033e4a0a0902287836533 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 31 Oct 2016 10:55:37 +0100 Subject: [PATCH 242/350] missing ' added --- easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb index 41dae6b7a6..45f3d738e8 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb @@ -49,7 +49,7 @@ dependencies = [ configopts = 'MOC=$EBROOTQT/bin/moc ' configopts += 'UIC=$EBROOTQT/bin/uic ' -configopts += 'RCC=$EBROOTQT/bin/rcc +configopts += 'RCC=$EBROOTQT/bin/rcc ' configopts += 'LRELEASE=$EBROOTQT/bin/lrelease ' configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' -- GitLab From c9ad017d3aeafb11f679650f324a5e997a923df9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 2 Nov 2016 16:19:22 +0100 Subject: [PATCH 243/350] Add an easyconfig for the behave software. This is a nice little piece of software. We use it for our vasp test suite, developed by Peter Larsson, NSC LiU Description of behave: Behavior-driven development (or BDD) is an agile software development technique that encourages collaboration between developers, QA and non-technical or business participants in a software project. --- .../behave-1.2.5-foss-2016b-Python-2.7.12.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3a5ba505f6 --- /dev/null +++ b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'behave' +version = '1.2.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +homepage = 'https://pypi.python.org/packages' +description = """behave: Behavior-driven development (or BDD) is an +agile software development technique that encourages collaboration +between developers, QA and non-technical or business participants in a +software project.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +# ('py', '1.4.31', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' + -- GitLab From cc7f38b34919cf3b509889d107eaab4dffae1e43 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 2 Nov 2016 16:29:27 +0100 Subject: [PATCH 244/350] Add an intel-cuda toolchain. Modeled after the goolfc toolchain. Depends on framework PR# 1976 --- ...0.44-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 19 ++++++++++ .../i/iccifortcuda/iccifortcuda-2016.10.0.eb | 24 ++++++++++++ .../easyconfigs/i/iimpic/iimpic-2016.10.0.eb | 23 +++++++++++ .../imkl/imkl-11.3.3.210-iimpic-2016.10.0.eb | 38 +++++++++++++++++++ .../impi-5.1.3.181-iccifortcuda-2016.10.0.eb | 35 +++++++++++++++++ .../easyconfigs/i/intelc/intelc-2016.10.0.eb | 27 +++++++++++++ 6 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-iccifort-2016.3.210-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.0.eb create mode 100644 easybuild/easyconfigs/i/iimpic/iimpic-2016.10.0.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.0.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.0.eb create mode 100644 easybuild/easyconfigs/i/intelc/intelc-2016.10.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..c0dc1eccdc --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44-iccifort-2016.3.210-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': 'iccifort', 'version': '2016.3.210-GCC-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/i/iccifortcuda/iccifortcuda-2016.10.0.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.0.eb new file mode 100644 index 0000000000..5e070ddc7c --- /dev/null +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'iccifortcuda' +version = '2016.10.0' + +homepage = '(none)' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'iccifort' +comp_ver = '2016.3.210' +gccver = '5.4.0' +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +cudacomp = (comp_name, '%s%s' % (comp_ver, gccsuff)) + +dependencies = [ + ('icc', comp_ver, gccsuff), + ('ifort', comp_ver, gccsuff), + ('CUDA', '8.0.44', '', cudacomp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.0.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.0.eb new file mode 100644 index 0000000000..7e4dd19038 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.0.eb @@ -0,0 +1,23 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpic' +version = '2016.10.0' + +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 = '2016.3.210' +suff = '-GCC-5.4.0-2.26' +comp = ('iccifort', '%s%s' % (compver, suff)) + +dependencies = [ + ('icc', compver, suff), + ('ifort', compver, suff), + ('CUDA', '8.0.44', '', comp), + ('impi', '5.1.3.181', '', ('iccifortcuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.0.eb new file mode 100644 index 0000000000..60d2bc76e1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.0.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': 'iimpic', 'version': '2016.10.0'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +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-5.1.3.181-iccifortcuda-2016.10.0.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.0.eb new file mode 100644 index 0000000000..0a845c6fbc --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.0.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '5.1.3.181' + +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': 'iccifortcuda', 'version': '2016.10.0'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +checksums = ['1c14656859d48bf8b90c71dace2a977b'] + +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' diff --git a/easybuild/easyconfigs/i/intelc/intelc-2016.10.0.eb b/easybuild/easyconfigs/i/intelc/intelc-2016.10.0.eb new file mode 100644 index 0000000000..38a1bb71af --- /dev/null +++ b/easybuild/easyconfigs/i/intelc/intelc-2016.10.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Toolchain' + +name = 'intelc' +version = '2016.10.0' + +homepage = '(none)' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'iccifort' +comp_ver = '2016.3.210' +gccver = '5.4.0' +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +comp = (comp_name, '%s%s' % (comp_ver, gccsuff)) + +dependencies = [ + comp, # part of iimpic + ('CUDA', '8.0.44', '', comp), + ('icc', comp_ver, gccsuff), + ('ifort', comp_ver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifortcuda', version)), + ('imkl', '11.3.3.210', '', ('iimpic', version)), +] + +moduleclass = 'toolchain' -- GitLab From 14075d37c186e7fbac183c605096e0d4b426c68d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 2 Nov 2016 23:37:49 +0100 Subject: [PATCH 245/350] add easyconfig SPAdes-3.9.0-foss-2016b.eb --- .../s/SPAdes/SPAdes-3.9.0-foss-2016b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016b.eb new file mode 100644 index 0000000000..a92f27ffac --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016b.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 +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "CMakeMake" + +name = 'SPAdes' +version = '3.9.0' + +homepage = 'http://bioinf.spbau.ru/en/spades' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://spades.bioinf.spbau.ru/release%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +start_dir = 'src' + +separate_build_dir = True + +configopts = ' -DBoost_NO_BOOST_CMAKE=ON' + +sanity_check_commands = [('spades.py', '--test')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bwa-spades", "dipspades", "dipspades.py", + "hammer", "ionhammer", "spades", "spades.py"]], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 2f03bf721bcdd5c89689e736e4a52c71bb108247 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 3 Nov 2016 00:08:52 +0100 Subject: [PATCH 246/350] add easyconfig Trim_Galore-0.4.2-foss-2016b.eb --- .../Trim_Galore-0.4.2-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb new file mode 100644 index 0000000000..b6070a5118 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb @@ -0,0 +1,33 @@ +# 0.4.2 modified by: +# Adam Huffman +# The Francis Crick Institute +# TODO: deal with the hardcoding of /usr/bin/perl + +easyblock = "PackedBinary" + +name = 'Trim_Galore' +version = '0.4.2' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """A wrapper tool around Cutadapt and FastQC to consistently apply + quality and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(namelower)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] + +install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" + +dependencies = [ + ('FastQC', '0.11.5', '-Java-1.7.0_80', True), + ('cutadapt', '1.9.1', '-Python-2.7.12'), +] + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From ff85ec5d9d7fa608b121ffb0402c7b6b0d9f1bd2 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 2 Nov 2016 16:12:54 -0700 Subject: [PATCH 247/350] 2nd try new module prokka --- .../BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb | 31 +++++++++++++ .../prokka-1.11-foss-2016b-BioPerl-1.7.0.eb | 43 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..dbed209e6f --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb @@ -0,0 +1,31 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center + +name = 'BioPerl' +version = '1.7.0' + +easyblock = 'PerlModule' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.zip' % version.replace('.', '-')] + +perl = 'Perl' +perlver = '5.24.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb b/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb new file mode 100644 index 0000000000..77c56eaa14 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb @@ -0,0 +1,43 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center + +easyblock = 'Tarball' + +name = 'prokka' + +version = '1.11' +versionsuffix = '-BioPerl-1.7.0' + +homepage = 'http://www.vicbioinformatics.com/software.prokka.shtml' +description = """Prokka is a software tool for the rapid annotation of prokaryotic genomes.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] + +dependencies = [('BioPerl', '1.7.0', '-Perl-5.24.0')] + +modextrapaths = { + 'PATH': '', +} + +bin_files = ["prokka", "prokka-cdd_to_hmm", "prokka-genpept_to_fasta_db", "prokka-tigrfams_to_hmm", + "prokka-biocyc_to_fasta_db", "prokka-clusters_to_hmm", "prokka-hamap_to_hmm", + "prokka-uniprot_to_fasta_db", "prokka-build_kingdom_dbs", "prokka-genbank_to_fasta_db", "prokka-make_tarball"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in bin_files] + + ["binaries/linux/aragorn", + "db/cm/Bacteria", + "doc/ToDoList.txt"], + 'dirs': ["bin", "binaries", + "db", "db/cm","db/genus","db/hmm","db/kingdom", + "doc" ], +} + +modloadmsg = '''prokka scripts are located in \\$EBROOTPROKKA/bin Databases are located: \\$EBROOTPROKKA/db''' + +moduleclass = 'bio' -- GitLab From 9029cd51e2f3b416ba4b60b9d8109aaa7e654efb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 3 Nov 2016 00:26:41 +0100 Subject: [PATCH 248/350] add easyconfig freetype-2.7-foss-2016b.eb, add easyconfig HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb, add easyconfig matplotlib-1.5.3-foss-2016b-Python-2.7.12.eb --- .../f/freetype/freetype-2.7-foss-2016b.eb | 26 +++++++++++ .../HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb | 27 ++++++++++++ ...tplotlib-1.5.3-foss-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb new file mode 100644 index 0000000000..8b88736d00 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7-foss-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': 'foss', '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/h/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..c7f13d0e1c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-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': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..64688cec7b --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.3-foss-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': 'foss', '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' -- GitLab From 887ff46d9609645bd545ee79be49339ae11b8b7a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 3 Nov 2016 08:03:02 +0100 Subject: [PATCH 249/350] Updated the homepage of behave and removed uncommented cruft. --- .../b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb index 3a5ba505f6..637bef0400 100644 --- a/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb @@ -4,8 +4,7 @@ name = 'behave' version = '1.2.5' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://pytest.org' -homepage = 'https://pypi.python.org/packages' +homepage = 'http://pythonhosted.org/behave' description = """behave: Behavior-driven development (or BDD) is an agile software development technique that encourages collaboration between developers, QA and non-technical or business participants in a @@ -18,7 +17,6 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.12'), -# ('py', '1.4.31', versionsuffix), ] sanity_check_paths = { -- GitLab From fa62e828b70df334e12e4740574a47db2a12ca8b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 3 Nov 2016 08:04:38 +0100 Subject: [PATCH 250/350] Drop empty line --- .../b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb index 637bef0400..515ba57589 100644 --- a/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/behave/behave-1.2.5-foss-2016b-Python-2.7.12.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'tools' - -- GitLab From 3aa16b4415fc8aee6556a46be4630e01209e0dfb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Nov 2016 11:16:20 +0100 Subject: [PATCH 251/350] style fixes for BioPerl and prokka easyconfigs --- .../BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb | 11 ++++----- .../prokka-1.11-foss-2016b-BioPerl-1.7.0.eb | 24 ++++++++----------- 2 files changed, 14 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb index dbed209e6f..4a78852736 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.0-foss-2016b-Perl-5.24.0.eb @@ -4,10 +4,11 @@ # # Fred Hutchinson Cancer Research Center +easyblock = 'PerlModule' + name = 'BioPerl' version = '1.7.0' - -easyblock = 'PerlModule' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://www.bioperl.org/' description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. @@ -18,12 +19,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] sources = ['release-%s.zip' % version.replace('.', '-')] -perl = 'Perl' -perlver = '5.24.0' -versionsuffix = '-%s-%s' % (perl, perlver) - dependencies = [ - (perl, perlver), + ('Perl', '5.24.0'), ] options = {'modulename': 'Bio::Perl'} diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb b/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb index 77c56eaa14..a9b5ed1e23 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.11-foss-2016b-BioPerl-1.7.0.eb @@ -6,9 +6,9 @@ easyblock = 'Tarball' name = 'prokka' - version = '1.11' -versionsuffix = '-BioPerl-1.7.0' +bioperl_ver = '1.7.0' +versionsuffix = '-BioPerl-%s' % bioperl_ver homepage = 'http://www.vicbioinformatics.com/software.prokka.shtml' description = """Prokka is a software tool for the rapid annotation of prokaryotic genomes.""" @@ -18,26 +18,22 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/tseemann/prokka/archive/'] sources = ['v%(version)s.zip'] -dependencies = [('BioPerl', '1.7.0', '-Perl-5.24.0')] +dependencies = [('BioPerl', bioperl_ver, '-Perl-5.24.0')] modextrapaths = { 'PATH': '', } -bin_files = ["prokka", "prokka-cdd_to_hmm", "prokka-genpept_to_fasta_db", "prokka-tigrfams_to_hmm", - "prokka-biocyc_to_fasta_db", "prokka-clusters_to_hmm", "prokka-hamap_to_hmm", - "prokka-uniprot_to_fasta_db", "prokka-build_kingdom_dbs", "prokka-genbank_to_fasta_db", "prokka-make_tarball"] +bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] sanity_check_paths = { - 'files': ["bin/%s" % x for x in bin_files] + - ["binaries/linux/aragorn", - "db/cm/Bacteria", - "doc/ToDoList.txt"], - 'dirs': ["bin", "binaries", - "db", "db/cm","db/genus","db/hmm","db/kingdom", - "doc" ], + 'files': ['bin/%s' % x for x in bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], } -modloadmsg = '''prokka scripts are located in \\$EBROOTPROKKA/bin Databases are located: \\$EBROOTPROKKA/db''' +modloadmsg = "prokka scripts are located in \\$EBROOTPROKKA/bin; databases are located in \\$EBROOTPROKKA/db" moduleclass = 'bio' -- GitLab From 522f92db00b83d434ce831910a45705e929457c1 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 3 Nov 2016 14:20:54 -0500 Subject: [PATCH 252/350] Added icc 2017-update1 easyconfig file --- .../i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..6400499a51 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-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 = '2017.1.132' + +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_update%(version_minor)s_composer_edition_for_cpp.tgz'] + +checksums = ['41a0e8850ebb5f7169076c89be743ee2'] + +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 = '/opt/easybuild/licenses/intel/license.lic' + +moduleclass = 'compiler' -- GitLab From e3a885652e563dd8cf0fcd7a93980f7d78489147 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 3 Nov 2016 14:21:56 -0500 Subject: [PATCH 253/350] Added ifort 2017-update1 easyconfig file --- .../ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..70f7fb91f8 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-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 = '2017.1.132' + +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_update%(version_minor)s_composer_edition_for_fortran.tgz'] + +checksums = ['612169f4b40cdded8e212bf097925e4f'] + +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 = '/opt/easybuild/licenses/intel/license.lic' + +moduleclass = 'compiler' -- GitLab From 1c230699a9cf2c81b080fb9fcfa22d6f7d8aab24 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 3 Nov 2016 14:23:01 -0500 Subject: [PATCH 254/350] Added iccifort 2017-update1 easyconfig file --- .../iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..8034a2a1e1 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-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 = '2017.1.132' +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' -- GitLab From 6ce9bbeee4e57ac909d42a6a1d8c86d1d291ab5c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 3 Nov 2016 14:25:31 -0500 Subject: [PATCH 255/350] Added impi 2017-update1 easyconfig file --- ....132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..b0c1ffaa40 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-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 = '2017.1.132' + +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': '2017.1.132-GCC-5.4.0-2.26'} + +sources = ['l_mpi_%(version)s.tgz'] + +checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +license_file = '/opt/easybuild/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 a8a8745b1e0e0248f7ef8586543793eafc0d5079 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 3 Nov 2016 14:26:06 -0500 Subject: [PATCH 256/350] Added iimpi 2017-update1 easyconfig file --- .../i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..97332c6ea3 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-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 = '2017.01' +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 = '2017.1.132' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' -- GitLab From 6d8b6c578342f29868a9852b945511039263b74f Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 3 Nov 2016 14:27:22 -0500 Subject: [PATCH 257/350] Added imkl 2017-update1 easyconfig file --- ...-2017.1.132-iimpi-2017.1-GCC-5.4.0-2.26.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.1-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.1-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..70845ad106 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.1-GCC-5.4.0-2.26.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '2017.1.132' + +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': '2017.01-GCC-5.4.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['7911c0f777c4cb04225bf4518088939e'] + +dontcreateinstalldir = 'True' + +license_file = '/opt/easybuild/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the 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_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' -- GitLab From 22fa0b3e1451a2c3cecd8367199f944f0cea5669 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 3 Nov 2016 14:28:22 -0500 Subject: [PATCH 258/350] Added intel 2017-update1 easyconfig file --- .../easyconfigs/i/intel/intel-2017.01.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel/intel-2017.01.eb diff --git a/easybuild/easyconfigs/i/intel/intel-2017.01.eb b/easybuild/easyconfigs/i/intel/intel-2017.01.eb new file mode 100644 index 0000000000..9993bc8e47 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017.01.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2017.01' + +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 = '2017.1.132' +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', compver, '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', compver, '', ('iimpi', version + gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From 1b5f19b4ad1802ba5fcae6837f64d9571d894550 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 3 Nov 2016 14:46:52 -0500 Subject: [PATCH 259/350] Fixed file typo --- ....0-2.26.eb => imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/imkl/{imkl-2017.1.132-iimpi-2017.1-GCC-5.4.0-2.26.eb => imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb} (100%) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb similarity index 100% rename from easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.1-GCC-5.4.0-2.26.eb rename to easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb -- GitLab From a0f8f589f0e6da736276e7447c01ed53e8b03b70 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 4 Nov 2016 14:03:08 -0500 Subject: [PATCH 260/350] Fixed license path --- easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb | 2 +- .../impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb index 6400499a51..924f53625d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' -license_file = '/opt/easybuild/licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb index 70f7fb91f8..a400dd9f38 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -28,6 +28,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' -license_file = '/opt/easybuild/licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb index 70845ad106..be8b68226a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -16,7 +16,7 @@ checksums = ['7911c0f777c4cb04225bf4518088939e'] dontcreateinstalldir = 'True' -license_file = '/opt/easybuild/licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index b0c1ffaa40..bebecd8cf6 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -18,7 +18,7 @@ dontcreateinstalldir = 'True' components = ['intel-mpi', 'intel-psxe', 'intel-imb'] -license_file = '/opt/easybuild/licenses/intel/license.lic' +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From 0357b31ee4a0bc1aba5bbc712400e21b2385bda3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Nov 2016 20:08:43 +0100 Subject: [PATCH 261/350] fix location/name of Anaconda easyconfig files --- .../{Anaconda/Anaconda2.4.0.0.eb => Anaconda2/Anaconda2-4.0.0.eb} | 0 .../{Anaconda/Anaconda3.4.0.0.eb => Anaconda3/Anaconda3-4.0.0.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/{Anaconda/Anaconda2.4.0.0.eb => Anaconda2/Anaconda2-4.0.0.eb} (100%) rename easybuild/easyconfigs/a/{Anaconda/Anaconda3.4.0.0.eb => Anaconda3/Anaconda3-4.0.0.eb} (100%) diff --git a/easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb similarity index 100% rename from easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb rename to easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb diff --git a/easybuild/easyconfigs/a/Anaconda/Anaconda3.4.0.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb similarity index 100% rename from easybuild/easyconfigs/a/Anaconda/Anaconda3.4.0.0.eb rename to easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb -- GitLab From 70b84a08f1614ac0b0bc4b1689870977ea0a5c99 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 4 Nov 2016 14:17:03 -0500 Subject: [PATCH 262/350] Added HPL 2.2 with intel-2017.01 easyconfig --- .../easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb new file mode 100644 index 0000000000..64700f3b27 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.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': '2017.01'} +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 f0e1a1abc2d7289aeb3d2914f54172164ac5a9b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Nov 2016 21:47:26 +0100 Subject: [PATCH 263/350] use generic CondaCreate easyblock, fix dep --- easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb b/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb index 378b53a6e2..258c1c0dbe 100644 --- a/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb +++ b/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb @@ -10,7 +10,7 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock = 'EB_CondaCreate' +easyblock = 'CondaCreate' name = "condacreate-module" version = "1.0" @@ -25,13 +25,13 @@ description = """ Conda is a platform- and packages. This repository hosts the corresponding recipes. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} requirements = "perl-app-cpanminus" channels = 'bioconda' post_install_cmd = "cpanm --notest ExtUtils::MakeMaker" -builddependencies = [('anaconda', '2-4.0.0')] +builddependencies = [('Anaconda2', '4.0.0')] sanity_check_paths = { 'files': ['bin/cpanm', 'bin/perl'], -- GitLab From cee69040e2a8613c8892b71ce8b4bb17b23982ec Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 7 Nov 2016 09:01:01 +0100 Subject: [PATCH 264/350] add easyconfig Rosetta-3.7-foss-2016b.eb, add easyconfig SCons-2.5.0-foss-2016b-Python-2.7.12.eb --- .../r/Rosetta/Rosetta-3.7-foss-2016b.eb | 20 ++++++++++++++++ .../SCons-2.5.0-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.5.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb new file mode 100644 index 0000000000..dc1928028e --- /dev/null +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-3.7-foss-2016b.eb @@ -0,0 +1,20 @@ +name = 'Rosetta' +version = '3.7' + +homepage = 'https://www.rosettacommons.org' +description = """Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, +multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and +nucleic acids.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] + +builddependencies = [('SCons', '2.5.0', '-Python-2.7.12')] + +modextravars = { + 'ROSETTA3_DB': '$root/database', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f7cac2e6e2 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.0-foss-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': 'foss', '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 c34c659ebc4cb2f4023662a0fe3c0344772446e3 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 7 Nov 2016 11:05:58 +0100 Subject: [PATCH 265/350] latest InterProScan. Including required fix for centos6 systems --- .../InterProScan-5.21-60.0-intel-2015b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb new file mode 100644 index 0000000000..1169ea8d18 --- /dev/null +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'InterProScan' +version = '5.21-60.0' + +homepage = 'http://www.ebi.ac.uk/interpro/' +description = """InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines + different protein signature recognition methods into one resource.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/', + 'ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/bin/'] +sources = ['%(namelower)s-%(version)s-64-bit.tar.gz', 'sfld_binary.zip'] + +dependencies = [ + ('Java', '1.7.0_80', '', True), + ('Perl', '5.20.3'), + ('libgd', '2.1.1'), + ('Python', '2.7.10'), +] + +sanity_check_paths = { + 'files': ['interproscan-%(version_major)s.jar', 'interproscan.sh', 'interproscan.properties'], + 'dirs': ['bin', 'lib', 'data'], +} + +# Workaround required for CentOS 6 systems. Details here: +# https://github.com/ebi-pf-team/interproscan/issues/16 +postinstallcmds = ['cp -f %(builddir)s/sfld_postprocess %(installdir)s/bin/sfld/', + 'cp -f %(builddir)s/sfld_preprocess %(installdir)s/bin/sfld/'] + +moduleclass = 'bio' -- GitLab From f7583c12a5383ce6a20704b8aeec56fda20fda80 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 7 Nov 2016 14:01:08 +0100 Subject: [PATCH 266/350] add easyconfig MUMmer-3.23-foss-2016b.eb --- .../m/MUMmer/MUMmer-3.23-foss-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb new file mode 100644 index 0000000000..279406579d --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +name = 'MUMmer' +version = '3.23' + +homepage = 'http://mummer.sourceforge.net/' +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] + +moduleclass = 'bio' -- GitLab From 3fb3374e47e352e0072f9eb63d1edb7bdf24a2a6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 7 Nov 2016 15:35:43 +0100 Subject: [PATCH 267/350] Rewrite header of GROMACS-2016-foss-2016b-hybrid.eb --- .../g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb index 781809d07e..7099241376 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb @@ -1,15 +1,16 @@ ## # 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 +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman # 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 -- GitLab From b28335ce41287d21dde927f34484327f1a9284e4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 7 Nov 2016 18:28:45 +0100 Subject: [PATCH 268/350] Added "The Francis Crick Institute" to the Copyright notice. --- .../easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb index 7099241376..be709c1c8d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University / The Francis Crick Institute # Authors:: # * Wiktor Jurkowski # * Fotis Georgatos @@ -9,7 +9,6 @@ # * Kenneth Hoste # * Adam Huffman # License:: MIT/GPL -# $Id$ # # Version 5.1.4 # Author: Adam Huffman -- GitLab From 5665f85dfa683bc64efbafc95e0a376737ac2945 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Nov 2016 20:01:51 +0100 Subject: [PATCH 269/350] adding easyconfigs: Rust-1.12.1-foss-2016b.eb --- .../r/Rust/Rust-1.12.1-foss-2016b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb b/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb new file mode 100644 index 0000000000..a06ae54597 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.12.1' + +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', '2.7.12'), ('CMake','3.6.2')] + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' -- GitLab From 150f6d9c3ba5bac58b58fefe5cb30c3878acc10e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Nov 2016 20:18:00 +0100 Subject: [PATCH 270/350] adding easyconfigs: Cargo-0.1.0-foss-2016b.eb --- .../c/Cargo/Cargo-0.1.0-foss-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cargo/Cargo-0.1.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/Cargo/Cargo-0.1.0-foss-2016b.eb b/easybuild/easyconfigs/c/Cargo/Cargo-0.1.0-foss-2016b.eb new file mode 100644 index 0000000000..70ed1ad009 --- /dev/null +++ b/easybuild/easyconfigs/c/Cargo/Cargo-0.1.0-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Cargo' +version = '0.1.0' + +homepage = 'https://crates.io/' +description = "The Rust package manager" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/rust-lang/cargo/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Rust', '1.12.1'), +] +builddependencies = [ + ('CMake', '3.6.2'), + ('Python', '2.7.12'), + ('cURL', '7.49.1'), +] + +buildopts = 'VERBOSE=1' + +sanity_check_paths = { + 'files': [], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 3a7f2c437178482b5507070d818fbba0cc0d267b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 8 Nov 2016 02:05:17 +0100 Subject: [PATCH 271/350] add easyconfig BEDOPS-2.4.20.eb --- .../easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb new file mode 100644 index 0000000000..7bbeac455b --- /dev/null +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb @@ -0,0 +1,27 @@ +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'BEDOPS' +version = '2.4.20' + +homepage = 'http://bedops.readthedocs.io/en/latest/index.html' +description = """BEDOPS is an open-source command-line toolkit that performs highly efficient + and scalable Boolean and other set operations, statistical calculations, archiving, conversion + and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome + for distributing whole-genome analyses across a computational cluster.""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = ['%(namelower)s_linux_x86_64-v%(version)s.v2.tar.bz2'] +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] + +sanity_check_paths = { + 'files': ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch'], + 'dirs': ['.'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' -- GitLab From cb725b78d26afae7124c32f260af01d3b18ad189 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 8 Nov 2016 10:12:21 +0400 Subject: [PATCH 272/350] cleaning up configs --- .../easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb | 2 +- .../{CondaCreate => Conda}/condacreate-1.0.eb | 6 +++--- .../c/{CondaEnv => Conda}/condaenv-1.0.eb | 19 ++++++------------- .../c/{CondaEnv => Conda}/environment.yml | 0 4 files changed, 10 insertions(+), 17 deletions(-) rename easybuild/easyconfigs/c/{CondaCreate => Conda}/condacreate-1.0.eb (91%) rename easybuild/easyconfigs/c/{CondaEnv => Conda}/condaenv-1.0.eb (53%) rename easybuild/easyconfigs/c/{CondaEnv => Conda}/environment.yml (100%) diff --git a/easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb b/easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb index b5ffaf0935..95588e5f7a 100644 --- a/easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda/Anaconda2.4.0.0.eb @@ -14,6 +14,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] -checksums = ['31ed3ef07435d7068e1e03be49381b13' ] +#checksums = ['31ed3ef07435d7068e1e03be49381b13' ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb b/easybuild/easyconfigs/c/Conda/condacreate-1.0.eb similarity index 91% rename from easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb rename to easybuild/easyconfigs/c/Conda/condacreate-1.0.eb index 378b53a6e2..8ee91dee6b 100644 --- a/easybuild/easyconfigs/c/CondaCreate/condacreate-1.0.eb +++ b/easybuild/easyconfigs/c/Conda/condacreate-1.0.eb @@ -10,9 +10,9 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock = 'EB_CondaCreate' +easyblock = 'EB_Conda' -name = "condacreate-module" +name = "perl-app-cpanminus" version = "1.0" variant = "Linux-x86_64" @@ -31,7 +31,7 @@ requirements = "perl-app-cpanminus" channels = 'bioconda' post_install_cmd = "cpanm --notest ExtUtils::MakeMaker" -builddependencies = [('anaconda', '2-4.0.0')] +builddependencies = [('Anaconda3', '4.0.0')] sanity_check_paths = { 'files': ['bin/cpanm', 'bin/perl'], diff --git a/easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb b/easybuild/easyconfigs/c/Conda/condaenv-1.0.eb similarity index 53% rename from easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb rename to easybuild/easyconfigs/c/Conda/condaenv-1.0.eb index ca01537d2c..f6048caf0e 100644 --- a/easybuild/easyconfigs/c/CondaEnv/condaenv-1.0.eb +++ b/easybuild/easyconfigs/c/Conda/condaenv-1.0.eb @@ -10,31 +10,24 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock = 'EB_CondaEnv' +easyblock = 'EB_Conda' -name = "condaenv-module" +name = "gencore_variant_detection" version = "1.0" variant = "Linux-x86_64" -homepage = "https://github.com/bioconda/bioconda-recipes" -description = """ Conda is a platform- and - language-independent package manager that sports - easy distribution, installation and version - management of software. The bioconda channel is a - Conda channel providing bioinformatics related - packages. This repository hosts the corresponding - recipes. """ +homepage = "https://nyuad-cgsb.github.io/variant_detection/public/index.html" +description = """ This is a bundled install of many software packages for doing variant detection analysis. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -builddependencies = [('anaconda', '2-4.0.0')] +builddependencies = [('Anaconda3', '4.0.0')] #Use one of the following - either an environment.yml file or a remote environment definition #sources = ["environment.yml"] -#It is not necessary to specify your environment_file unless it is named something besides environment.yml #environment_file = sources[0] -remote_environment = "jerowe/gencore_python_1.0" +remote_environment = "nyuad-cgsb/gencore_variant_detection_1.0" sanity_check_paths = { 'files': ["bin/conda"], diff --git a/easybuild/easyconfigs/c/CondaEnv/environment.yml b/easybuild/easyconfigs/c/Conda/environment.yml similarity index 100% rename from easybuild/easyconfigs/c/CondaEnv/environment.yml rename to easybuild/easyconfigs/c/Conda/environment.yml -- GitLab From 9aa42c2fa654c9bce69cc543f1fd8344424da471 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 8 Nov 2016 10:16:58 +0400 Subject: [PATCH 273/350] round 2 cleanup --- .../{condaenv-1.0.eb => gencore_variant_detection-1.0.eb} | 0 .../{condacreate-1.0.eb => perl-app-cpanminus-1.7039.eb} | 8 ++++---- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/c/Conda/{condaenv-1.0.eb => gencore_variant_detection-1.0.eb} (100%) rename easybuild/easyconfigs/c/Conda/{condacreate-1.0.eb => perl-app-cpanminus-1.7039.eb} (88%) diff --git a/easybuild/easyconfigs/c/Conda/condaenv-1.0.eb b/easybuild/easyconfigs/c/Conda/gencore_variant_detection-1.0.eb similarity index 100% rename from easybuild/easyconfigs/c/Conda/condaenv-1.0.eb rename to easybuild/easyconfigs/c/Conda/gencore_variant_detection-1.0.eb diff --git a/easybuild/easyconfigs/c/Conda/condacreate-1.0.eb b/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb similarity index 88% rename from easybuild/easyconfigs/c/Conda/condacreate-1.0.eb rename to easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb index dff22de272..9e876ada58 100644 --- a/easybuild/easyconfigs/c/Conda/condacreate-1.0.eb +++ b/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb @@ -13,7 +13,7 @@ easyblock = 'EB_Conda' name = "perl-app-cpanminus" -version = "1.0" +version = "1.7039" variant = "Linux-x86_64" homepage = "https://github.com/bioconda/bioconda-recipes" @@ -27,9 +27,9 @@ description = """ Conda is a platform- and toolchain = {'name': 'dummy', 'version': ''} -requirements = "perl-app-cpanminus" -channels = 'bioconda' -post_install_cmd = "cpanm --notest ExtUtils::MakeMaker" +requirements = "perl-app-cpanminus=1.7039" +channels = ['bioconda'] +installopts = "&& cpanm --notest ExtUtils::MakeMaker" builddependencies = [('Anaconda2', '4.0.0')] -- GitLab From c88b6676d0b831d4e2b653cd566afa1bb9e32e31 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 8 Nov 2016 10:25:28 +0400 Subject: [PATCH 274/350] example of installopts with anaconda and conda configs --- easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb | 2 ++ easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb index 95588e5f7a..e44fcc0777 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -15,5 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] #checksums = ['31ed3ef07435d7068e1e03be49381b13' ] +# +installopts = " && conda install -y conda " #Update conda on install moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb index 9d77e1debf..783a19b6e6 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb @@ -16,4 +16,6 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['546d1f02597587c685fa890c1d713b51'] +installopts = " && conda install -y conda " #Update conda on install + moduleclass = 'lang' -- GitLab From 31fdff232fc1884f5c746ef3ef34f9b6060d3195 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 8 Nov 2016 12:33:31 +0400 Subject: [PATCH 275/350] fixing anaconda easyblock --- easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb index e44fcc0777..7f580ea182 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -14,8 +14,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] -#checksums = ['31ed3ef07435d7068e1e03be49381b13' ] -# -installopts = " && conda install -y conda " #Update conda on install +checksums = ['31ed3ef07435d7068e1e03be49381b13'] moduleclass = 'lang' -- GitLab From a2727e034b076f9da82757cc9292ad7e8cfe4a3c Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 8 Nov 2016 12:35:14 +0400 Subject: [PATCH 276/350] updating perl-app-cpanminus --- .../easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb index 9e876ada58..7c8ca89f0d 100644 --- a/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb +++ b/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb @@ -16,14 +16,8 @@ name = "perl-app-cpanminus" version = "1.7039" variant = "Linux-x86_64" -homepage = "https://github.com/bioconda/bioconda-recipes" -description = """ Conda is a platform- and - language-independent package manager that sports - easy distribution, installation and version - management of software. The bioconda channel is a - Conda channel providing bioinformatics related - packages. This repository hosts the corresponding - recipes. """ +homepage = "http://search.cpan.org/~miyagawa/Menlo-1.9003/script/cpanm-menlo" +description = """ cpanm - get, unpack build and install modules from CPAN """ toolchain = {'name': 'dummy', 'version': ''} -- GitLab From f3d473ec98518e0a1a66f4b0dae54d0da6fbc1f7 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 8 Nov 2016 12:35:57 +0400 Subject: [PATCH 277/350] updating perl-app-cpanminus --- easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb index 7c8ca89f0d..c89b4f646e 100644 --- a/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb +++ b/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb @@ -21,7 +21,7 @@ description = """ cpanm - get, unpack build and install modules from CPAN """ toolchain = {'name': 'dummy', 'version': ''} -requirements = "perl-app-cpanminus=1.7039" +requirements = "%(name)s=%(version)s" channels = ['bioconda'] installopts = "&& cpanm --notest ExtUtils::MakeMaker" -- GitLab From 9625a60e072b50815e2e36dbd3276c5023e8b9a5 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 8 Nov 2016 12:43:31 +0400 Subject: [PATCH 278/350] still cleaning --- easybuild/easyconfigs/c/Conda/gencore_variant_detection-1.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Conda/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/c/Conda/gencore_variant_detection-1.0.eb index f6048caf0e..9cf70a3ec4 100644 --- a/easybuild/easyconfigs/c/Conda/gencore_variant_detection-1.0.eb +++ b/easybuild/easyconfigs/c/Conda/gencore_variant_detection-1.0.eb @@ -27,7 +27,8 @@ builddependencies = [('Anaconda3', '4.0.0')] #sources = ["environment.yml"] #environment_file = sources[0] -remote_environment = "nyuad-cgsb/gencore_variant_detection_1.0" +#remote_environment = "nyuad-cgsb/gencore_variant_detection_1.0" +remote_environment = "nyuad-cgsb/%(name)s_%(version)s" sanity_check_paths = { 'files': ["bin/conda"], -- GitLab From 2e092b2b2025191b3810f80e2bb8132fa1710bbd Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 8 Nov 2016 12:51:02 +0400 Subject: [PATCH 279/350] more cleanup --- easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb | 2 -- easybuild/easyconfigs/c/Conda/environment.yml | 5 ----- .../gencore_variant_detection-1.0.eb | 0 .../perl_app_cpanminus}/perl-app-cpanminus-1.7039.eb | 1 - 4 files changed, 8 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Conda/environment.yml rename easybuild/easyconfigs/{c/Conda => g/gencore_variant_detection}/gencore_variant_detection-1.0.eb (100%) rename easybuild/easyconfigs/{c/Conda => p/perl_app_cpanminus}/perl-app-cpanminus-1.7039.eb (94%) diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb index 783a19b6e6..9d77e1debf 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb @@ -16,6 +16,4 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['546d1f02597587c685fa890c1d713b51'] -installopts = " && conda install -y conda " #Update conda on install - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/Conda/environment.yml b/easybuild/easyconfigs/c/Conda/environment.yml deleted file mode 100644 index d98bf281fe..0000000000 --- a/easybuild/easyconfigs/c/Conda/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -name: variant_test -channels: - - bioconda -dependencies: - - samtools=1.3.1 diff --git a/easybuild/easyconfigs/c/Conda/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb similarity index 100% rename from easybuild/easyconfigs/c/Conda/gencore_variant_detection-1.0.eb rename to easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb diff --git a/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb similarity index 94% rename from easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb rename to easybuild/easyconfigs/p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb index c89b4f646e..52ac06d71d 100644 --- a/easybuild/easyconfigs/c/Conda/perl-app-cpanminus-1.7039.eb +++ b/easybuild/easyconfigs/p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb @@ -23,7 +23,6 @@ toolchain = {'name': 'dummy', 'version': ''} requirements = "%(name)s=%(version)s" channels = ['bioconda'] -installopts = "&& cpanm --notest ExtUtils::MakeMaker" builddependencies = [('Anaconda2', '4.0.0')] -- GitLab From fdbbc384f7ff9df9b2e75c9a6cc6309a75289e1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2016 10:12:22 +0100 Subject: [PATCH 280/350] use http mirror, add checksums + style fixes in InterProScan easyconfig --- .../InterProScan-5.21-60.0-intel-2015b.eb | 27 +++++++++++++------ 1 file changed, 19 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb index 1169ea8d18..2388f28009 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb @@ -9,9 +9,18 @@ description = """InterProScan is a sequence analysis application (nucleotide and toolchain = {'name': 'intel', 'version': '2015b'} -source_urls = ['http://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/', - 'ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/bin/'] -sources = ['%(namelower)s-%(version)s-64-bit.tar.gz', 'sfld_binary.zip'] +source_urls = [ + 'http://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/', + 'http://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/bin/', +] +sources = [ + '%(namelower)s-%(version)s-64-bit.tar.gz', + 'sfld_binary.zip', +] +checksums = [ + '8090ff00ba75bce1383a257ff2b8d196', + '17ff8224789b9f35dd9304dcb7dc6a68', +] dependencies = [ ('Java', '1.7.0_80', '', True), @@ -20,14 +29,16 @@ dependencies = [ ('Python', '2.7.10'), ] +# Workaround required for CentOS 6 systems. Details here: +# https://github.com/ebi-pf-team/interproscan/issues/16 +postinstallcmds = [ + "cp -f %(builddir)s/sfld_postprocess %(installdir)s/bin/sfld/", + "cp -f %(builddir)s/sfld_preprocess %(installdir)s/bin/sfld/", +] + sanity_check_paths = { 'files': ['interproscan-%(version_major)s.jar', 'interproscan.sh', 'interproscan.properties'], 'dirs': ['bin', 'lib', 'data'], } -# Workaround required for CentOS 6 systems. Details here: -# https://github.com/ebi-pf-team/interproscan/issues/16 -postinstallcmds = ['cp -f %(builddir)s/sfld_postprocess %(installdir)s/bin/sfld/', - 'cp -f %(builddir)s/sfld_preprocess %(installdir)s/bin/sfld/'] - moduleclass = 'bio' -- GitLab From 2ee3ba017602fd2296c59a2938379625cf14c4af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2016 12:10:16 +0100 Subject: [PATCH 281/350] bump version to 0.13.0, also put rust-installer in place --- .../c/Cargo/Cargo-0.13.0-foss-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb b/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb new file mode 100644 index 0000000000..d05303a090 --- /dev/null +++ b/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Cargo' +version = '0.13.0' + +homepage = 'https://crates.io/' +description = "The Rust package manager" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'https://github.com/rust-lang/cargo/archive/', + 'https://github.com/rust-lang/rust-installer/archive/', +] +sources = [ + '%(version)s.tar.gz', + '4f99485.tar.gz', # rust-installer +] + +dependencies = [ + ('Rust', '1.12.1'), +] +builddependencies = [ + ('CMake', '3.6.2'), + ('Python', '2.7.12'), + ('cURL', '7.49.1'), +] + +buildopts = 'VERBOSE=1' +# rust-installer is a git submodule, but not included in the sources pulled from GitHub +preinstallopts = "cp -a %(builddir)s/rust-installer*/* %(builddir)s/cargo-%(version)s/src/rust-installer && " + +sanity_check_paths = { + 'files': ['bin/cargo'], + 'dirs': ['etc', 'lib/rustlib', 'share'], +} + +moduleclass = 'tools' -- GitLab From 8a5936b4a877f8a1eda13a70a160426cf75cbb43 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2016 12:25:15 +0100 Subject: [PATCH 282/350] also patch value for WM_PROJECT_VERSION in etc/bashrc and etc/cshrc for OpenFOAM 3.0.1 --- .../o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch index 335b44903b..9111c18ae3 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1_cleanup.patch @@ -44,6 +44,28 @@ diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/applications/utilities/postProcessing wmake libso vtkPV4Readers PV4blockMeshReader/Allwmake +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/bashrc 2016-11-08 12:21:21.478604080 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/bashrc 2016-11-08 12:21:27.978572000 +0100 +@@ -32,7 +32,7 @@ + #------------------------------------------------------------------------------ + + export WM_PROJECT=OpenFOAM +-export WM_PROJECT_VERSION=3.0.x ++export WM_PROJECT_VERSION=3.0.1 + + ################################################################################ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade +--- OpenFOAM-3.0.x-version-3.0.1.orig/etc/cshrc 2016-11-08 12:21:43.478604102 +0100 ++++ OpenFOAM-3.0.x-version-3.0.1/etc/cshrc 2016-11-08 12:21:50.258390000 +0100 +@@ -31,7 +31,7 @@ + #------------------------------------------------------------------------------ + + setenv WM_PROJECT OpenFOAM +-setenv WM_PROJECT_VERSION 3.0.x ++setenv WM_PROJECT_VERSION 3.0.1 + + ################################################################################ + # USER EDITABLE PART: Changes made here may be lost with the next upgrade diff -ru OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/CGAL.sh OpenFOAM-3.0.x-version-3.0.1/etc/config/CGAL.sh --- OpenFOAM-3.0.x-version-3.0.1.orig/etc/config/CGAL.sh 2015-12-15 12:20:08.000000000 +0100 +++ OpenFOAM-3.0.x-version-3.0.1/etc/config/CGAL.sh 2016-10-25 12:04:22.000000000 +0200 -- GitLab From 9f3d0746bbb15b3cdc971b241c728611834e2011 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2016 12:29:33 +0100 Subject: [PATCH 283/350] remove easyconfig for ancient Cargo version --- .../c/Cargo/Cargo-0.1.0-foss-2016b.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Cargo/Cargo-0.1.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/Cargo/Cargo-0.1.0-foss-2016b.eb b/easybuild/easyconfigs/c/Cargo/Cargo-0.1.0-foss-2016b.eb deleted file mode 100644 index 70ed1ad009..0000000000 --- a/easybuild/easyconfigs/c/Cargo/Cargo-0.1.0-foss-2016b.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Cargo' -version = '0.1.0' - -homepage = 'https://crates.io/' -description = "The Rust package manager" - -toolchain = {'name': 'foss', 'version': '2016b'} - -source_urls = ['https://github.com/rust-lang/cargo/archive/'] -sources = ['%(version)s.tar.gz'] - -dependencies = [ - ('Rust', '1.12.1'), -] -builddependencies = [ - ('CMake', '3.6.2'), - ('Python', '2.7.12'), - ('cURL', '7.49.1'), -] - -buildopts = 'VERBOSE=1' - -sanity_check_paths = { - 'files': [], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From db3ec68d8733f0ee32c7ae8f20d1acd0b01619d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2016 13:59:13 +0100 Subject: [PATCH 284/350] add pointer to upstream issue for rust-installer problem --- easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb b/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb index d05303a090..fc872af329 100644 --- a/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb +++ b/easybuild/easyconfigs/c/Cargo/Cargo-0.13.0-foss-2016b.eb @@ -28,6 +28,7 @@ builddependencies = [ buildopts = 'VERBOSE=1' # rust-installer is a git submodule, but not included in the sources pulled from GitHub +# see also https://github.com/rust-lang/cargo/issues/2130 preinstallopts = "cp -a %(builddir)s/rust-installer*/* %(builddir)s/cargo-%(version)s/src/rust-installer && " sanity_check_paths = { -- GitLab From ec3621857cd7ddb068e78f7e40c3133ba881759d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2016 14:59:30 +0100 Subject: [PATCH 285/350] stick to flex 2.5.39 with OpenFOAM 3.0.1, it is not compatible with flex 2.6.0 yet --- .../easyconfigs/f/flex/flex-2.5.39-intel-2016b.eb | 14 ++++++++++++++ .../o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb | 2 +- 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016b.eb new file mode 100644 index 0000000000..d599b0583d --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2016b.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb index e27c7e7895..065d8bedfb 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb @@ -30,7 +30,7 @@ dependencies = [ builddependencies = [ ('Bison', '3.0.4'), ('CMake', '3.6.1'), - ('flex', '2.6.0'), + ('flex', '2.5.39'), ] moduleclass = 'cae' -- GitLab From e43d00a903658298da32fe325f6fd4ae75d0bd34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2016 15:14:21 +0100 Subject: [PATCH 286/350] adding easyconfigs: flex-2.6.2-intel-2016b.eb, help2man-1.47.4-intel-2016b.eb --- .../f/flex/flex-2.6.2-intel-2016b.eb | 22 +++++++++++++++++++ .../h/help2man/help2man-1.47.4-intel-2016b.eb | 19 ++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.2-intel-2016b.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.2-intel-2016b.eb b/easybuild/easyconfigs/f/flex/flex-2.6.2-intel-2016b.eb new file mode 100644 index 0000000000..ac6504cacf --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.2-intel-2016b.eb @@ -0,0 +1,22 @@ +name = 'flex' +version = '2.6.2' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['cc6d76c333db7653d5caf423a3335239'] + +dependencies = [('M4', '1.4.17')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-intel-2016b.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-intel-2016b.eb new file mode 100644 index 0000000000..53cf30b69c --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-intel-2016b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 6e20a17bed9a0f34a248ae504fc4039d4c98f09e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2016 11:49:21 +0100 Subject: [PATCH 287/350] adding easyconfigs: Gurobi-6.5.2.eb, Gurobi-7.0.1.eb --- easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb new file mode 100644 index 0000000000..fdd1e676ca --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb @@ -0,0 +1,18 @@ +name = 'Gurobi' +version = '6.5.2' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# registration is required +# source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb new file mode 100644 index 0000000000..758e95aed3 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb @@ -0,0 +1,18 @@ +name = 'Gurobi' +version = '7.0.1' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# registration is required +# source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +moduleclass = 'math' -- GitLab From ac0a0befaf904d69d369768fdd9407b651fe849e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 9 Nov 2016 12:54:09 +0100 Subject: [PATCH 288/350] SPAdes 3.9.0 with foss 2016a --- .../s/SPAdes/SPAdes-3.9.0-foss-2016a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016a.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016a.eb new file mode 100644 index 0000000000..af3845c60d --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-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 +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "CMakeMake" + +name = 'SPAdes' +version = '3.9.0' + +homepage = 'http://bioinf.spbau.ru/en/spades' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://spades.bioinf.spbau.ru/release%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +start_dir = 'src' + +separate_build_dir = True + +configopts = ' -DBoost_NO_BOOST_CMAKE=ON' + +sanity_check_commands = [('spades.py', '--test')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bwa-spades", "dipspades", "dipspades.py", + "hammer", "ionhammer", "spades", "spades.py"]], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 7ad3c0ac69aeec873d5f7fc9ed299a85b6dffc9a Mon Sep 17 00:00:00 2001 From: Ole Holm Nielsen Date: Wed, 9 Nov 2016 13:24:41 +0100 Subject: [PATCH 289/350] iomkl toolchain with GCC-5.4.0-2.26 and OpenMPI 1.10.3 --- ...11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb | 36 +++++++++++++++++++ .../i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb | 20 +++++++++++ .../i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb | 20 +++++++++++ 3 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..4739cbc290 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.09-GCC-5.4.0-2.26.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': '2016.09-GCC-5.4.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +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-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..6b0377e8e3 --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '2016.09-GCC-5.4.0-2.26' + +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-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..6ab1a7b7d5 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iompi' +version = '2016.09-GCC-5.4.0-2.26' + +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 = [ + ('OpenMPI', '1.10.3', '', ('iccifort', compver)), + ('icc', compver), + ('ifort', compver), +] + +moduleclass = 'toolchain' + -- GitLab From 5ff21d258552657d968bb1e0db073d32734e51a0 Mon Sep 17 00:00:00 2001 From: Ole Holm Nielsen Date: Wed, 9 Nov 2016 15:59:02 +0100 Subject: [PATCH 290/350] HPL test module for the iomkl-2016.09-GCC-5.4.0-2.26 toolchain --- .../HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..efda5a282c --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.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-5.4.0-2.26'} +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 2090cf95d5727cdd7f33c4467063e4f4c84e2573 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Nov 2016 13:18:03 +0100 Subject: [PATCH 291/350] update Travis config w.r.t. changes framework config defaults and required Lmod version --- .travis.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 1100abe24e..253f7f158c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,16 +2,18 @@ language: python python: 2.6 env: matrix: - - ENV_MOD_VERSION=3.2.10 - - LMOD_VERSION=5.6.3 EASYBUILD_MODULES_TOOL=Lmod - - LMOD_VERSION=6.3.1 EASYBUILD_MODULES_TOOL=Lmod EASYBUILD_MODULE_SYNTAX=Lua + - ENV_MOD_VERSION=3.2.10 EASYBUILD_MODULES_TOOL=EnvironmentModulesC EASYBUILD_MODULE_SYNTAX=Tcl + - LMOD_VERSION=5.8 + - LMOD_VERSION=5.8 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=6.6.2 + - LMOD_VERSION=6.6.2 EASYBUILD_MODULE_SYNTAX=Lua matrix: # mark build as finished as soon as job has failed fast_finish: true include: # also test default configuration with Python 2.7 - python: 2.7 - env: ENV_MOD_VERSION=3.2.10 + env: LMOD_VERSION=5.8 addons: apt: packages: -- GitLab From 42df09c2e4730096cc1d7a63147a1c03347aa25e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 10 Nov 2016 14:00:22 +0100 Subject: [PATCH 292/350] Rename the top level Intel+CUDA toolchain to intelcuda --- .../i/intelc/{intelc-2016.10.0.eb => intelcuda-2016.10.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/i/intelc/{intelc-2016.10.0.eb => intelcuda-2016.10.0.eb} (97%) diff --git a/easybuild/easyconfigs/i/intelc/intelc-2016.10.0.eb b/easybuild/easyconfigs/i/intelc/intelcuda-2016.10.0.eb similarity index 97% rename from easybuild/easyconfigs/i/intelc/intelc-2016.10.0.eb rename to easybuild/easyconfigs/i/intelc/intelcuda-2016.10.0.eb index 38a1bb71af..6ba471c5d6 100644 --- a/easybuild/easyconfigs/i/intelc/intelc-2016.10.0.eb +++ b/easybuild/easyconfigs/i/intelc/intelcuda-2016.10.0.eb @@ -1,6 +1,6 @@ easyblock = 'Toolchain' -name = 'intelc' +name = 'intelcuda' version = '2016.10.0' homepage = '(none)' -- GitLab From 1d0c31be46e5810c1f370bc31e07112313582714 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 10 Nov 2016 17:09:33 +0100 Subject: [PATCH 293/350] MrBayes 3.2.6 with foss/2016a --- .../m/MrBayes/MrBayes-3.2.6-foss-2016a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb new file mode 100644 index 0000000000..03307965e4 --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'MrBayes' +version = '3.2.6' + +homepage = 'http://mrbayes.csit.fsu.edu' +description = "MrBayes is a program for the Bayesian estimation of phylogeny." + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%(version)s"] + +dependencies = [ + ('beagle-lib', '2.1.2'), + ('libreadline', '6.3'), +] + +builddependencies = [ + ('Autoconf', '2.69'), +] + +moduleclass = 'bio' -- GitLab From 62624b4d2e3d1906e7902a93ddd4f4cb9de1960d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Nov 2016 20:58:22 +0100 Subject: [PATCH 294/350] add HPL easyconfig for intelcuda toolchain + reversion it to 2016.10 --- .../h/HPL/HPL-2.2-intelcuda-2016.10.eb | 18 ++++++++++++++++++ ...da-2016.10.0.eb => iccifortcuda-2016.10.eb} | 2 +- .../{iimpic-2016.10.0.eb => iimpic-2016.10.eb} | 2 +- ....0.eb => imkl-11.3.3.210-iimpic-2016.10.eb} | 2 +- ... => impi-5.1.3.181-iccifortcuda-2016.10.eb} | 2 +- .../intelcuda-2016.10.eb} | 2 +- 6 files changed, 23 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb rename easybuild/easyconfigs/i/iccifortcuda/{iccifortcuda-2016.10.0.eb => iccifortcuda-2016.10.eb} (96%) rename easybuild/easyconfigs/i/iimpic/{iimpic-2016.10.0.eb => iimpic-2016.10.eb} (96%) rename easybuild/easyconfigs/i/imkl/{imkl-11.3.3.210-iimpic-2016.10.0.eb => imkl-11.3.3.210-iimpic-2016.10.eb} (96%) rename easybuild/easyconfigs/i/impi/{impi-5.1.3.181-iccifortcuda-2016.10.0.eb => impi-5.1.3.181-iccifortcuda-2016.10.eb} (95%) rename easybuild/easyconfigs/i/{intelc/intelcuda-2016.10.0.eb => intelcuda/intelcuda-2016.10.eb} (97%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb new file mode 100644 index 0000000000..05f316bde4 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.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': 'intelcuda', 'version': '2016.10'} +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' diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.0.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb similarity index 96% rename from easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.0.eb rename to easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb index 5e070ddc7c..1eeb749c6e 100644 --- a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.0.eb +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'iccifortcuda' -version = '2016.10.0' +version = '2016.10' homepage = '(none)' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.0.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb similarity index 96% rename from easybuild/easyconfigs/i/iimpic/iimpic-2016.10.0.eb rename to easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb index 7e4dd19038..33bf002bbf 100644 --- a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.0.eb +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb @@ -2,7 +2,7 @@ easyblock = "Toolchain" name = 'iimpic' -version = '2016.10.0' +version = '2016.10' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb similarity index 96% rename from easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.0.eb rename to easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb index 60d2bc76e1..601460577a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'iimpic', 'version': '2016.10.0'} +toolchain = {'name': 'iimpic', 'version': '2016.10'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['f72546df27f5ebb0941b5d21fd804e34'] diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.0.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb similarity index 95% rename from easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.0.eb rename to easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb index 0a845c6fbc..292b8c704e 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag 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': 'iccifortcuda', 'version': '2016.10.0'} +toolchain = {'name': 'iccifortcuda', 'version': '2016.10'} sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/intelc/intelcuda-2016.10.0.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb similarity index 97% rename from easybuild/easyconfigs/i/intelc/intelcuda-2016.10.0.eb rename to easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb index 6ba471c5d6..ac6a734e6e 100644 --- a/easybuild/easyconfigs/i/intelc/intelcuda-2016.10.0.eb +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'intelcuda' -version = '2016.10.0' +version = '2016.10' homepage = '(none)' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" -- GitLab From d0f600fadd054a2d4cd6c996d2311373387c90b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Nov 2016 21:11:50 +0100 Subject: [PATCH 295/350] reversion goolfc 2016.10.0 to goolfc 2016.10 + add HPL easyconfig as testcase --- ...16.10.0.eb => FFTW-3.3.5-gompic-2016.10.eb} | 2 +- ...gcccuda-2016.10.0.eb => gcccuda-2016.10.eb} | 2 +- .../{gompic-2016.10.0.eb => gompic-2016.10.eb} | 2 +- .../{goolfc-2016.10.0.eb => goolfc-2016.10.eb} | 2 +- .../h/HPL/HPL-2.2-goolfc-2016.10.eb | 18 ++++++++++++++++++ ...10.0.eb => hwloc-1.11.4-gcccuda-2016.10.eb} | 2 +- ....0.eb => numactl-2.0.11-gcccuda-2016.10.eb} | 2 +- ...BLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb} | 2 +- ...0.0.eb => OpenMPI-2.0.1-gcccuda-2016.10.eb} | 2 +- ...ic-2016.10-OpenBLAS-0.2.19-LAPACK-3.6.1.eb} | 2 +- 10 files changed, 27 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.5-gompic-2016.10.0.eb => FFTW-3.3.5-gompic-2016.10.eb} (95%) rename easybuild/easyconfigs/g/gcccuda/{gcccuda-2016.10.0.eb => gcccuda-2016.10.eb} (94%) rename easybuild/easyconfigs/g/gompic/{gompic-2016.10.0.eb => gompic-2016.10.eb} (96%) rename easybuild/easyconfigs/g/goolfc/{goolfc-2016.10.0.eb => goolfc-2016.10.eb} (98%) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb rename easybuild/easyconfigs/h/hwloc/{hwloc-1.11.4-gcccuda-2016.10.0.eb => hwloc-1.11.4-gcccuda-2016.10.eb} (94%) rename easybuild/easyconfigs/n/numactl/{numactl-2.0.11-gcccuda-2016.10.0.eb => numactl-2.0.11-gcccuda-2016.10.eb} (93%) rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.2.19-gompic-2016.10.0-LAPACK-3.6.1.eb => OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb} (96%) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-2.0.1-gcccuda-2016.10.0.eb => OpenMPI-2.0.1-gcccuda-2016.10.eb} (95%) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompic-2016.10.0-OpenBLAS-0.2.19-LAPACK-3.6.1.eb => ScaLAPACK-2.0.2-gompic-2016.10-OpenBLAS-0.2.19-LAPACK-3.6.1.eb} (91%) 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.eb similarity index 95% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.0.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-gompic-2016.10.eb index 6df05f5634..2499d7f87a 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.eb @@ -7,7 +7,7 @@ homepage = 'http://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'gompic', 'version': '2016.10.0'} +toolchain = {'name': 'gompic', 'version': '2016.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.0.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb similarity index 94% rename from easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.0.eb rename to easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb index 3d0ba0c9cf..ddfec681fb 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.0.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'gcccuda' -version = '2016.10.0' +version = '2016.10' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" diff --git a/easybuild/easyconfigs/g/gompic/gompic-2016.10.0.eb b/easybuild/easyconfigs/g/gompic/gompic-2016.10.eb similarity index 96% rename from easybuild/easyconfigs/g/gompic/gompic-2016.10.0.eb rename to easybuild/easyconfigs/g/gompic/gompic-2016.10.eb index b0c994f8de..39f562c6fb 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2016.10.0.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2016.10.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'gompic' -version = '2016.10.0' +version = '2016.10' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.0.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb similarity index 98% rename from easybuild/easyconfigs/g/goolfc/goolfc-2016.10.0.eb rename to easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb index 6fd9d7c78b..4ee5c6f696 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.0.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'goolfc' -version = '2016.10.0' +version = '2016.10' homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb new file mode 100644 index 0000000000..fff961832d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.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': 'goolfc', 'version': '2016.10'} +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' 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.eb similarity index 94% rename from easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.0.eb rename to easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb index 20cd96a781..a83862d853 100644 --- 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.eb @@ -11,7 +11,7 @@ system attributes such as cache and memory information as well as the locality o 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'} +toolchain = {'name': 'gcccuda', 'version': '2016.10'} source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] 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.eb similarity index 93% rename from easybuild/easyconfigs/n/numactl/numactl-2.0.11-gcccuda-2016.10.0.eb rename to easybuild/easyconfigs/n/numactl/numactl-2.0.11-gcccuda-2016.10.eb index 6ee99ec4e4..b6d4718450 100644 --- 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.eb @@ -8,7 +8,7 @@ description = """The numactl program allows you to run your application program 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'} +toolchain = {'name': 'gcccuda', 'version': '2016.10'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] 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-LAPACK-3.6.1.eb similarity index 96% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10.0-LAPACK-3.6.1.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb index 665e61e6ba..0102d20b13 100644 --- 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-LAPACK-3.6.1.eb @@ -9,7 +9,7 @@ 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'} +toolchain = {'name': 'gompic', 'version': '2016.10'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' 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.eb similarity index 95% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.0.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb index c4792dca19..3d626a7c80 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.eb @@ -6,7 +6,7 @@ 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'} +toolchain = {'name': 'gcccuda', 'version': '2016.10'} sources = [SOURCELOWER_TAR_GZ] 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-OpenBLAS-0.2.19-LAPACK-3.6.1.eb similarity index 91% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.10.0-OpenBLAS-0.2.19-LAPACK-3.6.1.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2016.10-OpenBLAS-0.2.19-LAPACK-3.6.1.eb index dabe226ac2..a4526fee65 100644 --- 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-OpenBLAS-0.2.19-LAPACK-3.6.1.eb @@ -5,7 +5,7 @@ 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'} +toolchain = {'name': 'gompic', 'version': '2016.10'} toolchainopts = {'pic': True} source_urls = [homepage] -- GitLab From d2fe76856c1b3cd088e23fe9a72917e4ed34a3e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Nov 2016 00:38:31 +0100 Subject: [PATCH 296/350] remove maxparallel in GCCcore easyconfigs --- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb | 3 --- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 3 --- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb | 3 --- easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 3 --- easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb | 3 --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 3 --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 3 --- 7 files changed, 21 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb index 01f4776c64..872c6745e0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb @@ -42,7 +42,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index a4f11a8fbd..d0d9f1d3a7 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -41,7 +41,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb index 1a8e12a57a..9a01aa75ef 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb @@ -41,7 +41,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index 1f2fc04edb..5c9d24095b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -48,7 +48,4 @@ 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-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index 5b9a17485e..54a7c67482 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -48,7 +48,4 @@ 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.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index 5b9af4041a..23873c04ec 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -51,7 +51,4 @@ 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-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index a375f0e539..61ee8bd066 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -50,7 +50,4 @@ 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' -- GitLab From 773d63d43018756141c205c9bcb98e671f7c8caf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Nov 2016 00:39:22 +0100 Subject: [PATCH 297/350] remove maxparallel in GCC 5.x easyconfigs --- easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb | 3 --- 4 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index 8bbf0ea88e..4385f0e569 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -49,7 +49,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index a69c58da2c..335fdafa66 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -43,7 +43,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb index c25b63f7b1..7db4c1240f 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -43,7 +43,4 @@ languages = ['c', 'c++', 'fortran'] withisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb index 83ebb4cb78..553ae6554a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb @@ -43,7 +43,4 @@ 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' -- GitLab From e4e2fb9c954e01bc8bb982e58dd1b6528dbbad8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Nov 2016 00:39:53 +0100 Subject: [PATCH 298/350] remove maxparallel in GCC 4.9.x easyconfigs --- easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb | 3 --- 12 files changed, 36 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb index f77a70efc3..6b00ed1249 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb @@ -48,7 +48,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb index 9974833bba..a3369e962d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb @@ -46,7 +46,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb index cd09534c39..288754285b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb @@ -34,7 +34,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb index a3c67d644e..7205bfb68b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb @@ -48,7 +48,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb index b78ac53014..816dca9804 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb @@ -46,7 +46,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb index 21e41342d3..d520b55ace 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb @@ -34,7 +34,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb index 0906283ab2..3bf02cbff3 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb @@ -48,7 +48,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb index 1af6bd9c36..65fefc78d2 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb @@ -46,7 +46,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb index 4985b9228e..44e39d233d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb @@ -39,7 +39,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index cb9f3aa4f2..e9df0050c0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -34,7 +34,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb index d762426d06..8c62c13920 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb @@ -39,7 +39,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb index 759f134bcc..e36af87104 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -34,7 +34,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' -- GitLab From 122a5fe537b3b548fc6d27b879415be865a53788 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Nov 2016 00:40:15 +0100 Subject: [PATCH 299/350] remove maxparallel in GCC 4.8.x easyconfigs --- easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb | 3 --- easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb | 3 --- 12 files changed, 36 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb index 97ecab725e..921e398b74 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb @@ -41,7 +41,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb index 18a5c26a04..85085960e8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb index 0cc4d2d8be..7b8edef7eb 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb @@ -43,7 +43,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb index 76ee08688e..de973e9d18 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb @@ -41,7 +41,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb index 45168e2586..8154896aaa 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb @@ -32,7 +32,4 @@ languages = ['c', 'c++', 'fortran'] multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb index 4f8e1b941b..525d8bbaf4 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb index 8f71a86f5f..49654a4965 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb @@ -43,7 +43,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb index 10a1ebfca0..d300b36d8f 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb index a553c070ef..39bb9b0ddb 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb @@ -43,7 +43,4 @@ clooguseisl = True multilib = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb index 7dd0f5df24..6d7c5cab94 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb @@ -41,7 +41,4 @@ withcloog = True withisl = True clooguseisl = True -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb index 5ac47478fb..5149d85b52 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb index 8618661532..358952fcd9 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -29,7 +29,4 @@ checksums = [ languages = ['c', 'c++', 'fortran'] -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - moduleclass = 'compiler' -- GitLab From c5ccd4254e9fcacef372d527006beee6bde96e69 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 12 Nov 2016 01:14:06 +0100 Subject: [PATCH 300/350] add easyconfig R-3.2.3-foss-2016b.eb, add easyconfig libjpeg-turbo-1.4.2-foss-2016b.eb, add easyconfig NASM-2.11.08-foss-2016b.eb --- .../libjpeg-turbo-1.4.2-foss-2016b.eb | 30 ++ .../n/NASM/NASM-2.11.08-foss-2016b.eb | 31 ++ .../easyconfigs/r/R/R-3.2.3-foss-2016b.eb | 449 ++++++++++++++++++ 3 files changed, 510 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016b.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016b.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016b.eb new file mode 100644 index 0000000000..f5e74640f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.2-foss-2016b.eb @@ -0,0 +1,30 @@ +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': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +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/n/NASM/NASM-2.11.08-foss-2016b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016b.eb new file mode 100644 index 0000000000..72c77d6685 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-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 = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb new file mode 100644 index 0000000000..004c178582 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -0,0 +1,449 @@ +name = 'R' +version = '3.2.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('libpng', '1.6.23'), # for plotting in R + ('libjpeg-turbo', '1.4.2'), # for plottting in R + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.5'), # for tcltk + ('Tk', '8.6.5'), # for tcltk + ('cURL', '7.49.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.0'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal + ('GMP', '6.1.1'), # for igraph +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 21st 2016 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', ext_options), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.3', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.9', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2.1', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5.1', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-22', ext_options), + ('mime', '0.4', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.1', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-3', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.60.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.3', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-4', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', 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'0.5-1', ext_options), + ('mboost', '2.5-0', ext_options), + ('msm', '1.6', ext_options), + ('nor1mix', '1.2-1', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('polspline', '1.1.12', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-1', ext_options), + ('rms', '4.4-1', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-11', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-5', ext_options), + ('statmod', '1.4.23', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.3-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('optparse', '1.3.2', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '1.0.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.50.1', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-10', ext_options), + ('pbkrtest', '0.4-4', ext_options), + ('car', '2.1-1', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.31.4', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-10', ext_options), + ('BiasedUrn', '1.07', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '1.1', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.9.1', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.1.3', ext_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('VennDiagram', '1.6.16', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-2', ext_options), + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.8-37', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.44-1', ext_options), + ('rgdal', '1.1-3', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.8.8', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-4', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), + ('SuperLearner', '2.0-15', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('caret', '6.0-64', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.6', ext_options), + ('ggvis', '0.4.2', ext_options), + ('mlr', '2.7', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-7', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.10', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.4.0', ext_options), + ('roxygen2', '5.0.1', ext_options), + ('git2r', '0.13.1', ext_options), + ('xml2', '0.1.2', ext_options), + ('rversions', '1.0.2', ext_options), + ('devtools', '1.9.1', ext_options), + ('Rook', '1.1-1', ext_options), + ('rjson', '0.2.15', ext_options), + ('Cairo', '1.5-9', ext_options), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.1-6', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-7', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-9', ext_options), + ('ks', '1.10.1', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-45', ext_options), + ('coin', '1.1-2', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.0.7', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.5.8', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-20', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.8-6', ext_options), + ('mi', '1.0', ext_options), + ('htmlwidgets', '0.6', ext_options), + ('visNetwork', '0.2.1', ext_options), + ('DiagrammeR', '0.8.2', ext_options), + ('sem', '3.1-6', ext_options), + ('jpeg', '0.1-8', ext_options), + ('sna', '2.3-2', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.3.2', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.2', ext_options), + ('geepack', '1.2-0.1', ext_options), + ('lubridate', '1.5.6', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), +] + +moduleclass = 'lang' -- GitLab From b84622e961d8d77f5027f539a493e9bd1a183edf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2016 20:26:55 +0100 Subject: [PATCH 301/350] avoid specifying subtoolchain for flex/Bison build deps --- easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb | 4 ++-- easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb index 9aa1e31e3d..c060125491 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb @@ -24,8 +24,8 @@ dependencies = [ ] builddependencies = [ - ('flex', '2.5.39', '', ('GNU', '4.9.3-2.25')), - ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), ] # don't use parallel make, results in compilation failure diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb index ec3d535442..6b6b4181f9 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb @@ -24,8 +24,8 @@ dependencies = [ ] builddependencies = [ - ('flex', '2.5.39', '', ('GNU', '4.9.3-2.25')), - ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), + ('flex', '2.5.39'), + ('Bison', '3.0.4'), ] # don't use parallel make, results in compilation failure diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb index 3f2d3b24f6..0e52dfb998 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb @@ -15,6 +15,6 @@ checksums = [ 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] -dependencies = [('M4', '1.4.17', '', ('GNU', '4.9.3-2.25'))] +dependencies = [('M4', '1.4.17')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb index cc528417f1..c1b7ac5006 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb @@ -15,6 +15,6 @@ checksums = [ 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] -dependencies = [('M4', '1.4.17', '', ('GNU', '4.9.3-2.25'))] +dependencies = [('M4', '1.4.17')] moduleclass = 'lang' -- GitLab From b194854e3b36c3e5b4e0f70cbf99159494057087 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2016 20:56:45 +0100 Subject: [PATCH 302/350] Revert "avoid specifying subtoolchain for flex/Bison build deps" This reverts commit b84622e961d8d77f5027f539a493e9bd1a183edf. --- easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb | 4 ++-- easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb index c060125491..9aa1e31e3d 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb @@ -24,8 +24,8 @@ dependencies = [ ] builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.4'), + ('flex', '2.5.39', '', ('GNU', '4.9.3-2.25')), + ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), ] # don't use parallel make, results in compilation failure diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb index 6b6b4181f9..ec3d535442 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb @@ -24,8 +24,8 @@ dependencies = [ ] builddependencies = [ - ('flex', '2.5.39'), - ('Bison', '3.0.4'), + ('flex', '2.5.39', '', ('GNU', '4.9.3-2.25')), + ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), ] # don't use parallel make, results in compilation failure diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb index 0e52dfb998..3f2d3b24f6 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb @@ -15,6 +15,6 @@ checksums = [ 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] -dependencies = [('M4', '1.4.17')] +dependencies = [('M4', '1.4.17', '', ('GNU', '4.9.3-2.25'))] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb index c1b7ac5006..cc528417f1 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb @@ -15,6 +15,6 @@ checksums = [ 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz ] -dependencies = [('M4', '1.4.17')] +dependencies = [('M4', '1.4.17', '', ('GNU', '4.9.3-2.25'))] moduleclass = 'lang' -- GitLab From b779f4246b807359aa013337c8e0c077c2a693d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2016 21:59:16 +0100 Subject: [PATCH 303/350] revert back changes to archived easyconfig --- .../__archive__/f/flex/flex-2.5.39-intel-para-2014.12.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/f/flex/flex-2.5.39-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/f/flex/flex-2.5.39-intel-para-2014.12.eb index 09e533d59d..7cd93ab5fc 100644 --- a/easybuild/easyconfigs/__archive__/f/flex/flex-2.5.39-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/__archive__/f/flex/flex-2.5.39-intel-para-2014.12.eb @@ -11,10 +11,4 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -checksums = [ - 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz -] - -dependencies = [('M4', '1.4.17')] - moduleclass = 'lang' -- GitLab From 8f0b2e226823d8c62fa25ef7d05a7b518c6d01eb Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sat, 12 Nov 2016 23:16:22 +0100 Subject: [PATCH 304/350] add easyconfig Minimac2-2014.9.15-goolf-1.7.20.eb --- .../Minimac2-2014.9.15-goolf-1.7.20.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb new file mode 100644 index 0000000000..79a432c81f --- /dev/null +++ b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb @@ -0,0 +1,50 @@ +# 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 = 'Minimac2' +version = '2014.9.15' + +homepage = 'http://genome.sph.umich.edu/wiki/Minimac2' +description = """minimac2 is an improved version of Minimac. It is designed to work on phased + genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. + The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. + The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://csg.sph.umich.edu/cfuchsb/'] +sources = ['%(namelower)s.%(version)s.src.tgz'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +dependencies = [ + ('zlib', '1.2.8'), + # This app also depends in openblas +# ('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 +] + +# firt move to folder libStatGen to run make clean && make +# make clean is mandatory because the sources tarball includes +# files from previous build +prebuildopts = ["cd libStatGen && make clean && "] + +# in libStatGen folder run just "make" +# in minimac folder run "make clean && make opt && make openmp" +buildopts = [" && cd ../minimac2 && make clean && make opt && make openmp"] + +# parallel build fails +parallel = 1 + +files_to_copy = [(["minimac2/bin/minimac2", "minimac2/bin/minimac2-omp"], "bin")] + +sanity_check_paths = { + 'files': ['bin/minimac2', 'bin/minimac2-omp'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From ff6c08e6c3161b50a77a6fc785cdcd4056fc1c21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Nov 2016 16:41:24 +0100 Subject: [PATCH 305/350] adding easyconfigs: Advisor-2017_update1.eb --- .../a/Advisor/Advisor-2017_update1.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb new file mode 100644 index 0000000000..89c1628d39 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb @@ -0,0 +1,21 @@ +name = 'Advisor' +version = '2017_update1' + +homepage = 'https://software.intel.com/intel-advisor-xe' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['advisor_%(version)s.tar.gz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'perf' -- GitLab From 45866919751baf48bc4fb645870cb7347fb32561 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Nov 2016 21:13:28 +0100 Subject: [PATCH 306/350] use 'Conda' easyblock + empty version for dummy toolchain + some minor enhancements --- .../gencore_variant_detection-1.0.eb | 11 ++++------- .../p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb | 4 ++-- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb index 9cf70a3ec4..b799146d37 100644 --- a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb +++ b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb @@ -10,7 +10,7 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock = 'EB_Conda' +easyblock = 'Conda' name = "gencore_variant_detection" version = "1.0" @@ -19,15 +19,12 @@ variant = "Linux-x86_64" homepage = "https://nyuad-cgsb.github.io/variant_detection/public/index.html" description = """ This is a bundled install of many software packages for doing variant detection analysis. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} builddependencies = [('Anaconda3', '4.0.0')] -#Use one of the following - either an environment.yml file or a remote environment definition -#sources = ["environment.yml"] -#environment_file = sources[0] - -#remote_environment = "nyuad-cgsb/gencore_variant_detection_1.0" +# Use one of the following - either an environment.yml file or a remote environment definition +#environment_file = '/path/to/conda-environment.yml' remote_environment = "nyuad-cgsb/%(name)s_%(version)s" sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb index 52ac06d71d..c89d3af9f2 100644 --- a/easybuild/easyconfigs/p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb +++ b/easybuild/easyconfigs/p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb @@ -10,13 +10,13 @@ # http://apps.fz-juelich.de/unite/ ## -easyblock = 'EB_Conda' +easyblock = 'Conda' name = "perl-app-cpanminus" version = "1.7039" variant = "Linux-x86_64" -homepage = "http://search.cpan.org/~miyagawa/Menlo-1.9003/script/cpanm-menlo" +homepage = 'https://github.com/miyagawa/cpanminus' description = """ cpanm - get, unpack build and install modules from CPAN """ toolchain = {'name': 'dummy', 'version': ''} -- GitLab From ba67817bf19488e9efb8005ec902fa1a7ae8dca3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 11:16:50 +0100 Subject: [PATCH 307/350] {data}[intel/2016b] PyTables 3.3.0 w/ Python 2.7.12 + Python 3.5.2 (+ rename pyTables to PyTables) --- ...numexpr-2.6.1-intel-2016b-Python-2.7.12.eb | 27 ++++++++++++++ .../numexpr-2.6.1-intel-2016b-Python-3.5.2.eb | 27 ++++++++++++++ ...yTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb} | 2 +- .../PyTables-3.2.2-fix-libs.patch} | 0 ...Tables-3.2.2-intel-2015b-Python-2.7.10.eb} | 16 +++----- ...yTables-3.3.0-intel-2016b-Python-2.7.12.eb | 37 +++++++++++++++++++ ...PyTables-3.3.0-intel-2016b-Python-3.5.2.eb | 37 +++++++++++++++++++ 7 files changed, 135 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-3.5.2.eb rename easybuild/easyconfigs/p/{pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb => PyTables/PyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb} (98%) rename easybuild/easyconfigs/p/{pyTables/pyTables-3.2.2-fix-libs.patch => PyTables/PyTables-3.2.2-fix-libs.patch} (100%) rename easybuild/easyconfigs/p/{pyTables/pyTables-3.2.2-intel-2015b-Python-2.7.10.eb => PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb} (79%) create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a7f59e992e --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..f2a2e65aae --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.5.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb similarity index 98% rename from easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb rename to easybuild/easyconfigs/p/PyTables/PyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb index 9295347947..2a4a817730 100644 --- a/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb @@ -1,6 +1,6 @@ easyblock = "PythonPackage" -name = 'pyTables' +name = 'PyTables' version = '3.0.0' homepage = 'http://www.pytables.org/moin' diff --git a/easybuild/easyconfigs/p/pyTables/pyTables-3.2.2-fix-libs.patch b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-fix-libs.patch similarity index 100% rename from easybuild/easyconfigs/p/pyTables/pyTables-3.2.2-fix-libs.patch rename to easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-fix-libs.patch diff --git a/easybuild/easyconfigs/p/pyTables/pyTables-3.2.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb similarity index 79% rename from easybuild/easyconfigs/p/pyTables/pyTables-3.2.2-intel-2015b-Python-2.7.10.eb rename to easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb index c7500dde1e..99a9cd56f0 100644 --- a/easybuild/easyconfigs/p/pyTables/pyTables-3.2.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb @@ -1,7 +1,8 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = 'pyTables' +name = 'PyTables' version = '3.2.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pytables.org' description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope @@ -18,15 +19,10 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/PyTables/PyTables/archive/'] sources = ['v.%(version)s.tar.gz'] -patches = ['pyTables-%(version)s-fix-libs.patch'] - -python = 'Python' -pythonver = '2.7.10' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) +patches = ['%(name)s-%(version)s-fix-libs.patch'] dependencies = [ - (python, pythonver), + ('Python', '2.7.10'), ('numpy', '1.10.4', versionsuffix), ('numexpr', '2.4.6', versionsuffix), ('HDF5', '1.8.13'), @@ -34,7 +30,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], - 'dirs': ['lib/python%s/site-packages' % pythonshortver], + 'dirs': ['lib/python%(pyshortver)ss/site-packages'], } options = {'modulename': 'tables'} diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..affa66b440 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v.%(version)s.tar.gz'] + +patches = ['%(name)s-3.2.2-fix-libs.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('numexpr', '2.6.1', versionsuffix), + ('HDF5', '1.8.17'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..afe7cea34d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v.%(version)s.tar.gz'] + +patches = ['%(name)s-%(version)s-fix-libs.patch'] + +dependencies = [ + ('Python', '3.5.2'), + ('numexpr', '2.6.1', versionsuffix), + ('HDF5', '1.8.17'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' -- GitLab From 41be148edf37c0776946abbe431f81b5f55e5e3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 11:29:31 +0100 Subject: [PATCH 308/350] adding easyconfigs: dask-0.12.0-intel-2016b-Python-2.7.12.eb, dask-0.12.0-intel-2016b-Python-3.5.2.eb, distributed-1.14.3-intel-2016b-Python-2.7.12.eb, distributed-1.14.3-intel-2016b-Python-3.5.2.eb --- .../dask-0.12.0-intel-2016b-Python-2.7.12.eb | 37 ++++++++++ .../dask-0.12.0-intel-2016b-Python-3.5.2.eb | 37 ++++++++++ ...ibuted-1.14.3-intel-2016b-Python-2.7.12.eb | 68 +++++++++++++++++++ ...ributed-1.14.3-intel-2016b-Python-3.5.2.eb | 68 +++++++++++++++++++ 4 files changed, 210 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0b49bfdbc1 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +easyblock = 'Bundle' + +name = 'dask' +version = '0.12.0' +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'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '2.7.12')] + +exts_list = [ + ('toolz', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], + }), +] + +# 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 = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..46b06c2e96 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.12.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,37 @@ +easyblock = 'Bundle' + +name = 'dask' +version = '0.12.0' +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'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '3.5.2')] + +exts_list = [ + ('toolz', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], + }), +] + +# 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 = 'data' diff --git a/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0e72d5ec34 --- /dev/null +++ b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,68 @@ +easyblock = 'Bundle' + +name = 'distributed' +version = '1.14.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://distributed.readthedocs.io/' +description = """Dask.distributed is a lightweight library for distributed computing in Python. + It extends both the concurrent.futures and dask APIs to moderate sized clusters.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('dask', '0.12.0', versionsuffix), +] + +exts_list = [ + ('zict', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], + }), + ('HeapDict', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/H/HeapDict'], + 'modulename': 'heapdict', + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('tblib', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], + }), + ('psutil', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'source_tmpl': 'psutil-%(version)s.zip', + }), + ('msgpack-python', '0.4.8', { + 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack-python'], + 'modulename': 'msgpack', + }), + ('locket', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/locket'], + }), + ('cloudpickle', '0.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], + }), +] + +# 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/dask-remote', 'bin/dask-scheduler', 'bin/dask-ssh', 'bin/dask-submit', 'bin/dask-worker', + 'bin/dcenter', 'bin/dcluster', 'bin/dscheduler', 'bin/dworker'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..82253f9f50 --- /dev/null +++ b/easybuild/easyconfigs/d/distributed/distributed-1.14.3-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,68 @@ +easyblock = 'Bundle' + +name = 'distributed' +version = '1.14.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://distributed.readthedocs.io/' +description = """Dask.distributed is a lightweight library for distributed computing in Python. + It extends both the concurrent.futures and dask APIs to moderate sized clusters.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('dask', '0.12.0', versionsuffix), +] + +exts_list = [ + ('zict', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], + }), + ('HeapDict', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/H/HeapDict'], + 'modulename': 'heapdict', + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('tblib', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], + }), + ('psutil', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'source_tmpl': 'psutil-%(version)s.zip', + }), + ('msgpack-python', '0.4.8', { + 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack-python'], + 'modulename': 'msgpack', + }), + ('locket', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/locket'], + }), + ('cloudpickle', '0.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], + }), +] + +# 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/dask-remote', 'bin/dask-scheduler', 'bin/dask-ssh', 'bin/dask-submit', 'bin/dask-worker', + 'bin/dcenter', 'bin/dcluster', 'bin/dscheduler', 'bin/dworker'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' -- GitLab From 8fc459db7adfcf411581059cc08d8dd262431ad1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 11:31:19 +0100 Subject: [PATCH 309/350] adding easyconfigs: pandas-0.19.1-intel-2016b-Python-2.7.12.eb, pandas-0.19.1-intel-2016b-Python-3.5.2.eb --- ...pandas-0.19.1-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ .../pandas-0.19.1-intel-2016b-Python-3.5.2.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2d89267d1d --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.1' +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-0.19.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..15fd3118b3 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.19.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.19.1' +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 82f600675d3a5c72525c059dcfe015311070eeb6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 11:34:16 +0100 Subject: [PATCH 310/350] adding easyconfigs: IPython-5.1.0-intel-2016b-Python-3.5.2.eb, PyZMQ-15.4.0-intel-2016b-Python-3.5.2-zmq4.eb, entrypoints-0.2.2-intel-2016b-Python-3.5.2.eb, testpath-0.3-intel-2016b-Python-3.5.2.eb, path.py-8.2.1-intel-2016b-Python-3.5.2.eb, prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb, wcwidth-0.1.7-intel-2016b-Python-3.5.2.eb, configparser-3.5.0-intel-2016b-Python-3.5.2.eb --- ...igparser-3.5.0-intel-2016b-Python-3.5.2.eb | 32 ++++ ...rypoints-0.2.2-intel-2016b-Python-3.5.2.eb | 28 ++++ .../IPython-5.1.0-intel-2016b-Python-3.5.2.eb | 140 ++++++++++++++++++ ...MQ-15.4.0-intel-2016b-Python-3.5.2-zmq4.eb | 28 ++++ .../path.py-8.2.1-intel-2016b-Python-3.5.2.eb | 30 ++++ ...-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb | 30 ++++ .../testpath-0.3-intel-2016b-Python-3.5.2.eb | 27 ++++ .../wcwidth-0.1.7-intel-2016b-Python-3.5.2.eb | 27 ++++ 8 files changed, 342 insertions(+) create mode 100644 easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-3.5.2-zmq4.eb create mode 100644 easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..e3bb6d9e20 --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'configparser' +version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://docs.python.org/3/library/configparser.html' +description = "configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] +sources = ['configparser-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.5.2'), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('python', "-c 'import configparser'"), + ('python', "-c 'from backports import configparser'"), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..af5414eaac --- /dev/null +++ b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'entrypoints' +version = '0.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/takluyver/entrypoints' +description = """Entry points are a way for Python packages to advertise objects with some common interface.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/f8/ad/0e77a853c745a15981ab51fa9a0cb4eca7a7a007b4c1970106ee6ba01e0c/'] +sources = ['entrypoints-0.2.2-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), + ('configparser', '3.5.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/entrypoints.py'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..c1cf49347e --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,140 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('Python', '3.5.2'), + ('PyZMQ', '15.4.0', '%s-zmq4' % versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), + ('testpath', '0.3', versionsuffix), + ('path.py', '8.2.1', versionsuffix), + ('prompt-toolkit', '1.0.6', versionsuffix), +] + +# this is a bundle of Python packages +# XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have +# to be included as dependencies because bundling wheels does not work +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('requests', '2.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('certifi', '2016.8.8', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('jupyter_client', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools', '25.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pathlib2', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('pickleshare', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('nbconvert', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('decorator', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'patches': ['ipython-5.0.0_fix-test-paths-symlink.patch'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest3', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-3.5.2-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-3.5.2-zmq4.eb new file mode 100644 index 0000000000..f2cb970284 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-3.5.2-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.4.0' +zmqversion = '4.1.5' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..f558dad06a --- /dev/null +++ b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'path.py' +version = '8.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jaraco/path.py' +description = """path.py is a Python library implementing path objects as first-class entities, + allowing common operations on files to be invoked on those path objects directly.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/fc/fc/dcae2146aed6becbea77158eddb4e437718170efeade0f7fdf0aebe46b94/'] +sources = ['path.py-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/path.py'], + 'dirs': [], +} + +options = {'modulename': 'path'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..6c89475fe0 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '1.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/eb/81/a7ad3c223f323d05381208c262889bd09577852bd5044a13965a9a13f5ed/'] +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), + ('wcwidth', '0.1.7', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/prompt_toolkit'], +} + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..9ba2836ed4 --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'testpath' +version = '0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jupyter/testpath' +description = """Test utilities for code working with files and commands""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/testpath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..b18845a3b4 --- /dev/null +++ b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'wcwidth' +version = '0.1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jquast/wcwidth' +description = """wcwidth is a low-level Python library to simplify Terminal emulation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/'] +sources = ['%(name)s-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.2'), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/wcwidth'], +} + +moduleclass = 'lib' -- GitLab From cae639ef81e135fa4af275585ae290faee94da95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 11:39:49 +0100 Subject: [PATCH 311/350] bump Lmod test version to 6.6.3 since 6.6.2 was removed, also test against Lmod 7.0 --- .travis.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 253f7f158c..13ca5c0612 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,8 +5,10 @@ env: - ENV_MOD_VERSION=3.2.10 EASYBUILD_MODULES_TOOL=EnvironmentModulesC EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=5.8 - LMOD_VERSION=5.8 EASYBUILD_MODULE_SYNTAX=Lua - - LMOD_VERSION=6.6.2 - - LMOD_VERSION=6.6.2 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=6.6.3 + - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=7.0 + - LMOD_VERSION=7.0 EASYBUILD_MODULE_SYNTAX=Lua matrix: # mark build as finished as soon as job has failed fast_finish: true -- GitLab From 7364f1837a4681fcb19a3d6f32a456753e21a07c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 11:43:04 +0100 Subject: [PATCH 312/350] fix PyTables 3.3.0 version --- .../p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb | 2 +- .../p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb index affa66b440..e03818163d 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'PyTables' -version = '3.2.2' +version = '3.3.0' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pytables.org' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb index afe7cea34d..6465397fb5 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'PyTables' -version = '3.2.2' +version = '3.3.0' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pytables.org' -- GitLab From 96f5c09498f56be335d8b3da3ae299d6a007b0ba Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Tue, 15 Nov 2016 00:01:47 +1100 Subject: [PATCH 313/350] Update Yasm-1.3.0-goolf-1.7.20.eb --- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb index 250d77f32c..0e882e4bb6 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb @@ -2,7 +2,6 @@ easyblock = 'ConfigureMake' name = 'Yasm' version = '1.3.0' -#versionsuffix = '-20141219' description = "Yasm-1.3.0: Complete rewrite of the NASM assembler with BSD license" @@ -14,9 +13,7 @@ homepage = 'http://www.tortall.net/projects/yasm/' toolchain = {'name': 'goolf', 'version': '1.7.20'} sanity_check_paths = { - 'files': [], ## fixme - 'dirs': ['.'], ## fixme + 'dirs': ['bin/yasm'] } -parallel = 1 # this is a very conservative choice ## fixme -moduleclass = 'base' # please change this from base to right category ## fixme +moduleclass = 'lang' -- GitLab From a340c5084e75c5ab3fdd524722990d78220adc7a Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Tue, 15 Nov 2016 00:05:52 +1100 Subject: [PATCH 314/350] Update Yasm-1.3.0-goolf-1.7.20.eb --- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb index 0e882e4bb6..ac0261c145 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb @@ -5,7 +5,7 @@ version = '1.3.0' description = "Yasm-1.3.0: Complete rewrite of the NASM assembler with BSD license" -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.tortall.net/projects/yasm/releases/'] homepage = 'http://www.tortall.net/projects/yasm/' -- GitLab From d1df2dedefa8fd4a6d91051e10b1443437e991ce Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Tue, 15 Nov 2016 00:17:25 +1100 Subject: [PATCH 315/350] Update Yasm-1.3.0-goolf-1.7.20.eb --- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb index ac0261c145..09279b532a 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb @@ -3,17 +3,17 @@ easyblock = 'ConfigureMake' name = 'Yasm' version = '1.3.0' +homepage = 'http://www.tortall.net/projects/yasm/' description = "Yasm-1.3.0: Complete rewrite of the NASM assembler with BSD license" sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.tortall.net/projects/yasm/releases/'] -homepage = 'http://www.tortall.net/projects/yasm/' - toolchain = {'name': 'goolf', 'version': '1.7.20'} sanity_check_paths = { - 'dirs': ['bin/yasm'] + 'files': ['bin/yasm'], + 'dirs': [], } moduleclass = 'lang' -- GitLab From b25cabd2ff04cb59a12f26a7e14b849af205c046 Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Tue, 15 Nov 2016 00:57:08 +1100 Subject: [PATCH 316/350] Update x264-20160304-goolf-1.7.20.eb --- easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb index de24dff5a1..ecc982b174 100644 --- a/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb @@ -5,7 +5,7 @@ version = '20160304' 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.""" +AVC compression format, and is released under the terms of the GNU GPL.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -- GitLab From 6baaf48c2119e82e544f765adf5c1e3be6a940d3 Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Tue, 15 Nov 2016 01:09:29 +1100 Subject: [PATCH 317/350] Update x264-20160304-goolf-1.7.20.eb --- easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb index ecc982b174..063000f42c 100644 --- a/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb @@ -4,8 +4,7 @@ name = 'x264' version = '20160304' 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.""" +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': 'goolf', 'version': '1.7.20'} -- GitLab From 1d0ed982268eb9645c714e9ec194afe7219e8f1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 15:16:50 +0100 Subject: [PATCH 318/350] fix name of patch file for PyTables 3.3.0 --- .../p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb index 6465397fb5..076ef7198c 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb @@ -19,7 +19,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/PyTables/PyTables/archive/'] sources = ['v.%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s-fix-libs.patch'] +patches = ['pyTables-%(version)s-fix-libs.patch'] dependencies = [ ('Python', '3.5.2'), -- GitLab From 59a3c4de14880ac912fd7b7bc40d65ff6a889acd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 15:18:38 +0100 Subject: [PATCH 319/350] adding easyconfigs: bokeh-0.12.3-intel-2016b-Python-2.7.12.eb, bokeh-0.12.3-intel-2016b-Python-3.5.2.eb, PyYAML-3.12-intel-2016b-Python-2.7.12.eb --- .../bokeh-0.12.3-intel-2016b-Python-2.7.12.eb | 45 +++++++++++++++++++ .../bokeh-0.12.3-intel-2016b-Python-3.5.2.eb | 45 +++++++++++++++++++ .../PyYAML-3.12-intel-2016b-Python-2.7.12.eb | 27 +++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..aa1cb3dc2c --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'bokeh' +version = '0.12.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('PyYAML', '3.12', versionsuffix), +] + +exts_list = [ + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('requests', '2.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], + }), +] + +# 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/bokeh', 'bin/bokeh-server'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..84e9ec4ffb --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-0.12.3-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'bokeh' +version = '0.12.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.2'), + ('PyYAML', '3.12', versionsuffix), +] + +exts_list = [ + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('requests', '2.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests'], + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], + }), +] + +# 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/bokeh', 'bin/bokeh-server'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..72a7f70320 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +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.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('libyaml', '0.1.6'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From d7bf1037dc22711f0bc0ce6901b135bcd13aadd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 15:55:33 +0100 Subject: [PATCH 320/350] revert back name of PyTables patch file, correct source spec for PyTables v3.3.0 --- .../p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb | 2 +- .../p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb | 4 ++-- .../p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb | 2 +- ...les-3.2.2-fix-libs.patch => pyTables-3.2.2-fix-libs.patch} | 0 4 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/p/PyTables/{PyTables-3.2.2-fix-libs.patch => pyTables-3.2.2-fix-libs.patch} (100%) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb index 99a9cd56f0..51f246f954 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb @@ -19,7 +19,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/PyTables/PyTables/archive/'] sources = ['v.%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s-fix-libs.patch'] +patches = ['pyTables-%(version)s-fix-libs.patch'] dependencies = [ ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb index e03818163d..76d729b7ce 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb @@ -17,9 +17,9 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} source_urls = ['https://github.com/PyTables/PyTables/archive/'] -sources = ['v.%(version)s.tar.gz'] +sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-3.2.2-fix-libs.patch'] +patches = ['pyTables-3.2.2-fix-libs.patch'] dependencies = [ ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb index 076ef7198c..13bf11ff71 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True} source_urls = ['https://github.com/PyTables/PyTables/archive/'] -sources = ['v.%(version)s.tar.gz'] +sources = ['v%(version)s.tar.gz'] patches = ['pyTables-%(version)s-fix-libs.patch'] diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-fix-libs.patch b/easybuild/easyconfigs/p/PyTables/pyTables-3.2.2-fix-libs.patch similarity index 100% rename from easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-fix-libs.patch rename to easybuild/easyconfigs/p/PyTables/pyTables-3.2.2-fix-libs.patch -- GitLab From 6dc253d311b68b96565ec1c9d8eec112b6f17794 Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Tue, 15 Nov 2016 01:59:29 +1100 Subject: [PATCH 321/350] Update x264-20160304-goolf-1.7.20.eb --- easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb index 063000f42c..25aeefc81a 100644 --- a/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/x264/x264-20160304-goolf-1.7.20.eb @@ -4,7 +4,8 @@ name = 'x264' version = '20160304' 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.""" +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': 'goolf', 'version': '1.7.20'} -- GitLab From 9f5a322200a65ecbf390dc0275cd3fcebc373dd8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 16:14:16 +0100 Subject: [PATCH 322/350] fix patch for PyTables 3.3.0 --- .../p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb index 13bf11ff71..23f78177a2 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb @@ -19,7 +19,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/PyTables/PyTables/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['pyTables-%(version)s-fix-libs.patch'] +patches = ['pyTables-3.2.2-fix-libs.patch'] dependencies = [ ('Python', '3.5.2'), -- GitLab From e1d4ff136d18bc8be4373ac3c964c3c8df540d39 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 16:51:48 +0100 Subject: [PATCH 323/350] fix typo in PyTables easyconfig --- .../p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb index 51f246f954..554e1e9785 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-intel-2015b-Python-2.7.10.eb @@ -30,7 +30,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], - 'dirs': ['lib/python%(pyshortver)ss/site-packages'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } options = {'modulename': 'tables'} -- GitLab From 0c2f40116b639d14b71a88e85f36e0e38e22d666 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 14 Nov 2016 18:27:37 +0100 Subject: [PATCH 324/350] add easyconfig lbzip2-2.5-goolf-1.7.20.eb --- .../l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb new file mode 100644 index 0000000000..5abfa7b4da --- /dev/null +++ b/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb @@ -0,0 +1,27 @@ +# 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 = 'lbzip2' +version = '2.5' + +homepage = 'http://lbzip2.org/' +description = """lbzip2 is a free, multi-threaded compression utility with support for bzip2 compressed file format""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'openmp': True} + +source_urls = ['http://archive.lbzip2.org/'] +sources = [SOURCELOWER_TAR_GZ] + +buildopts = ' check' + +sanity_check_paths = { + 'files': ['bin/lbunzip2', 'bin/lbzcat', 'bin/lbzip2'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From bf9d3c1eeea81eb8c9b1578c87256635482feb4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 18:43:48 +0100 Subject: [PATCH 325/350] add LZO and Blosc as dependency in PyTables 3.3.0 easyconfigs --- .../b/Blosc/Blosc-1.11.1-intel-2016b.eb | 21 +++++++++++++ .../easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb | 31 +++++++++++++++++++ ...yTables-3.3.0-intel-2016b-Python-2.7.12.eb | 2 ++ ...PyTables-3.3.0-intel-2016b-Python-3.5.2.eb | 2 ++ 4 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.11.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.11.1-intel-2016b.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.11.1-intel-2016b.eb new file mode 100644 index 0000000000..088b4857b5 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.11.1-intel-2016b.eb @@ -0,0 +1,21 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.11.1' + +homepage = 'http://www.blosc.org/' +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.6.2')] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb b/easybuild/easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb new file mode 100644 index 0000000000..6e7ff8a596 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.09-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 +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.09' + +homepage = 'http://www.oberhumer.com/opensource/lzo/' +description = "LZO-2.06: Portable lossless data compression library" + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage + 'download/'] + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +runtest = 'test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb index 76d729b7ce..bb3c5f680e 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-2.7.12.eb @@ -25,6 +25,8 @@ dependencies = [ ('Python', '2.7.12'), ('numexpr', '2.6.1', versionsuffix), ('HDF5', '1.8.17'), + ('LZO', '2.09'), + ('Blosc', '1.11.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb index 23f78177a2..28dfb8ca71 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-intel-2016b-Python-3.5.2.eb @@ -25,6 +25,8 @@ dependencies = [ ('Python', '3.5.2'), ('numexpr', '2.6.1', versionsuffix), ('HDF5', '1.8.17'), + ('LZO', '2.09'), + ('Blosc', '1.11.1'), ] sanity_check_paths = { -- GitLab From 231c50d2af2463302730ff883bc04d0e957dc29b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 18:53:27 +0100 Subject: [PATCH 326/350] remove backports extensions from IPython 5.1.0 easyconfig --- .../i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb index c1cf49347e..c7fa3c0a41 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-3.5.2.eb @@ -48,9 +48,6 @@ exts_list = [ ('certifi', '2016.8.8', { 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], }), - ('backports_abc', '0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - }), ('tornado', '4.4.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], }), @@ -110,9 +107,6 @@ exts_list = [ ('nbconvert', '4.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], }), - ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], - }), ('decorator', '4.0.10', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), -- GitLab From 5a937cdb96c267b5c273ab6e2a4d8385df2bc85a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 18:55:49 +0100 Subject: [PATCH 327/350] consistently apply patch for ncurses 6.0 --- easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2016.03.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.eb | 2 ++ .../easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb | 2 ++ .../n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 2 ++ 12 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2016.03.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2016.03.eb index e38323ffda..307af92999 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2016.03.eb @@ -14,6 +14,8 @@ toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb index 02e4aae6ca..7d6659abd1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb index eab9da36db..52110246d2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-4.9.3.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + builddependencies = [('binutils', '2.25')] configopts = [ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb index 4012f0e69b..c1921a50bf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb index 6029357e96..8036d044c2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016a.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.eb index c9773784c0..2e3653e592 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.eb @@ -14,6 +14,8 @@ toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb index 7c1c8c34c6..06011329cd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016.02-GCC-4.9.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb index 852b0df6bb..ae49053391 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016a.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.eb index 2744e32733..d3393acd54 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.eb @@ -14,6 +14,8 @@ toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb index 77201153ed..98a4144e52 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.07.eb @@ -14,6 +14,8 @@ toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb index ab17db8531..12229c25b5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -14,6 +14,8 @@ toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite', diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index dcca941e16..ce06be716d 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] +patches = ['ncurses-%(version)s_gcc-5.patch'] + configopts = [ # default build '--with-shared --enable-overwrite --with-termlib', -- GitLab From b9ad02dbef6147ce8c5c946a425cf74e74e3bb9c Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 14 Nov 2016 13:00:42 -0500 Subject: [PATCH 328/350] Eliminate dependency on mpi-mic-rt in ifort. This dependency causes Intel mpirun/mpiexec to be added to $PATH when the ifort module is loaded, which is not always desirable, for instance when OpenMPI is already loaded. Fixes hpcugent/easybuild-easyblocks#1032. --- easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 3 +++ .../i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 +++ .../i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb | 3 +++ .../i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 3 +++ .../i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb | 3 +++ .../i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 3 +++ .../i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb | 3 +++ .../i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb | 3 +++ .../i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb | 3 +++ .../i/ifort/ifort_2017_no_mpi_mic_dependency.patch | 13 +++++++++++++ 10 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/ifort/ifort_2017_no_mpi_mic_dependency.patch diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index c64470205a..a32c4d179f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tg checksums = ['bce7f6a71f7e44f67956197501d00b7c'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + # 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 diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index aee6ae915e..bb6bb39f91 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['1e848c8283cf6a0210bce1d35ecd748b'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '4.9.3' binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index ffe995c4ac..37686bf975 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '4.9.3' binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 5844c8abd9..725d9d95e7 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70e88db11efc59b1d8ff8b5aadf50f7f'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '5.3.0' binutilsver = '2.26' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb index 303793bfad..8699c5d00e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '4.9.3' binutilsver = '2.25' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index b354753609..40c33c4e59 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '5.3.0' binutilsver = '2.26' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb index 29953965f2..33422fe405 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_up checksums = ['70cf1ea91280e3e8ba4bc216bae63e4a'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + gccver = '5.4.0' binutilsver = '2.26' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb index 9f30cbac75..a41293232b 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tg checksums = ['8787795951fe10f90ce7dcdcec1b9341'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] + gccver = '5.4.0' binutilsver = '2.26' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb index a400dd9f38..4493fad0d2 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -12,6 +12,9 @@ sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_compose checksums = ['612169f4b40cdded8e212bf097925e4f'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] + gccver = '5.4.0' binutilsver = '2.26' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/ifort/ifort_2017_no_mpi_mic_dependency.patch b/easybuild/easyconfigs/i/ifort/ifort_2017_no_mpi_mic_dependency.patch new file mode 100644 index 0000000000..8d3929a0f5 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort_2017_no_mpi_mic_dependency.patch @@ -0,0 +1,13 @@ +Eliminate dependency on intel-mpi-rt-mic which in turn brings in intel-mpi-rt. +author: Bart Oldeman (McGill HPC) +--- pset/mediaconfig.xml.orig 2016-10-20 09:02:57.000000000 +0000 ++++ pset/mediaconfig.xml 2016-11-11 20:09:08.084892189 +0000 +@@ -1551,7 +1551,7 @@ + ${BUNDLE_MAPFILE_DIR} + ${BUNDLE_CHKLIC_IA32} + +- ++ + Intel Fortran Compiler for Intel(R) 64 + Intel(R) Fortran Compiler 17.0 Update 1 + インテル(R) Fortran コンパイラー (インテル(R) 64) -- GitLab From dd1b6d3c2c2822fe53e86ba55c87c7f3c6b4f767 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 19:48:40 +0100 Subject: [PATCH 329/350] include Autotools as build dependency in all beagle-lib and MrBayes easyconfigs --- .../Autotools/Autotools-20150215-intel-2015a.eb | 17 +++++++++++++++++ .../beagle-lib-20120124-goolf-1.4.10.eb | 2 ++ .../beagle-lib-20120124-ictce-5.3.0.eb | 2 ++ .../beagle-lib-20141202-intel-2015a.eb | 6 ++---- .../l/libtool/libtool-2.4.6-intel-2015a.eb | 17 +++++++++++++++++ .../m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb | 9 +++++++-- .../m/MrBayes/MrBayes-3.1.2-ictce-5.3.0.eb | 9 ++++++--- .../m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb | 9 +++++++-- .../m/MrBayes/MrBayes-3.2.0-ictce-5.3.0.eb | 9 ++++++--- .../m/MrBayes/MrBayes-3.2.5-intel-2015a.eb | 8 ++++++-- .../m/MrBayes/MrBayes-3.2.6-foss-2016a.eb | 6 +++--- 11 files changed, 75 insertions(+), 19 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015a.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015a.eb new file mode 100644 index 0000000000..33124456f6 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2015a.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': 'intel', 'version': '2015a'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb index f54d71284a..bd2ca1ddb3 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb @@ -18,6 +18,8 @@ sources = [SOURCE_TGZ] dependencies = [('Java', '1.7.0_15', '', True)] +builddependencies = [('Autotools', '20150215')] + patches = ['beagle-lib-20120124_GCC-4.7.patch'] # parallel build does not work diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb index d4fc0c8fee..6d20b44133 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb @@ -16,6 +16,8 @@ sources = [SOURCE_TGZ] dependencies = [('Java', '1.7.0_15', '', True)] +builddependencies = [('Autotools', '20150215')] + # parallel build does not work parallel = 1 diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb index cc7febf444..0349d94e2a 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb @@ -15,10 +15,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [ - ('Java', '1.8.0_31', '', True), - ('Autoconf', '2.69') -] +dependencies = [('Java', '1.8.0_31', '', True)] +builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015a.eb new file mode 100644 index 0000000000..32d19e0439 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2015a.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': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb index faf00e5014..34b25f1567 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb @@ -3,15 +3,20 @@ version = '3.1.2' homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." + toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)] dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] +builddependencies = [ + ('Autotools', '20150215'), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-5.3.0.eb index 72d2021690..3e3e9603f2 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-ictce-5.3.0.eb @@ -4,16 +4,19 @@ version = '3.1.2' homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." - toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)] dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] +builddependencies = [ + ('Autotools', '20150215'), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb index a474900368..40b01594a5 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb @@ -3,15 +3,20 @@ version = '3.2.0' homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." + toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)] dependencies = [ ('beagle-lib', '20120124'), ('libreadline', '6.2'), ] +builddependencies = [ + ('Autotools', '20150215'), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-5.3.0.eb index 7ac8ffef36..79d0b7f304 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-ictce-5.3.0.eb @@ -4,16 +4,19 @@ version = '3.2.0' homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." - toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%s" % (version)] dependencies = [ ('beagle-lib', '20120124'), ('libreadline', '6.2'), ] +builddependencies = [ + ('Autotools', '20150215'), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb index 5836ec7f0f..421c44d0e5 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb @@ -5,14 +5,18 @@ homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%(version)s"] dependencies = [ ('beagle-lib', '20141202'), ('libreadline', '6.3'), ] +builddependencies = [ + ('Autotools', '20150215'), +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb index 03307965e4..e098f7c88a 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-foss-2016a.eb @@ -5,10 +5,10 @@ homepage = 'http://mrbayes.csit.fsu.edu' description = "MrBayes is a program for the Bayesian estimation of phylogeny." toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'usempi': True} +toolchainopts = {'usempi': True} +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%(version)s"] dependencies = [ ('beagle-lib', '2.1.2'), @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('Autoconf', '2.69'), + ('Autotools', '20150215'), ] moduleclass = 'bio' -- GitLab From cf10326c6a25733f6866ad4ade149d4596bd32e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 22:10:26 +0100 Subject: [PATCH 330/350] use Autotools built with GCC/4.7.2 toolchain as build dep for MrBayes/beagle-lib --- .../b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb index bd2ca1ddb3..eba16d5a4e 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb @@ -18,7 +18,7 @@ sources = [SOURCE_TGZ] dependencies = [('Java', '1.7.0_15', '', True)] -builddependencies = [('Autotools', '20150215')] +builddependencies = [('Autotools', '20150215', '', ('GCC', '4.7.2'))] patches = ['beagle-lib-20120124_GCC-4.7.patch'] diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb index 34b25f1567..85b5fe929e 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.1.2-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('Autotools', '20150215'), + ('Autotools', '20150215', '', ('GCC', '4.7.2')), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb index 40b01594a5..1ebf8b83b4 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.0-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('Autotools', '20150215'), + ('Autotools', '20150215', '', ('GCC', '4.7.2')), ] moduleclass = 'bio' -- GitLab From 60ba248bffea0f38aed8e33f2b915211ac50ee97 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 22:37:40 +0100 Subject: [PATCH 331/350] consistently make OpenBLAS use specified LAPACK version for versions 0.2.18 & 0.2.19 --- .../OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 8 ++++++-- .../OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb | 8 ++++++-- .../OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 2 +- .../OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb | 2 +- .../OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb | 2 +- .../OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb | 8 ++++++-- 6 files changed, 21 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb index d8f2e33a19..9dd493110f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -14,9 +14,14 @@ toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + sources = [ 'v%(version)s.tar.gz', - lapack_src, + (lapack_src, lapack_unpack_cmd), large_src, timing_src, ] @@ -28,7 +33,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb index 09e78a78ca..3879abb7bd 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb @@ -14,9 +14,14 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + sources = [ 'v%(version)s.tar.gz', - lapack_src, + (lapack_src, lapack_unpack_cmd), large_src, timing_src, ] @@ -28,7 +33,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb index eb1d2f67c9..21a2a7c815 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -15,7 +15,7 @@ lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -lapack_unpack_cmd = 'cd %s-%s; rm -rf lapack-netlib;' % (name, version) +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' 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 index 35ba0998f3..80a706fa33 100644 --- 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 @@ -15,7 +15,7 @@ lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -lapack_unpack_cmd = 'cd %s-%s; rm -rf lapack-netlib;' % (name, version) +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' 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 index 0755e77fbc..0978b24ced 100644 --- 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 @@ -15,7 +15,7 @@ lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -lapack_unpack_cmd = 'cd %s-%s; rm -rf lapack-netlib;' % (name, version) +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb index 0102d20b13..55794b4474 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb @@ -14,9 +14,14 @@ toolchain = {'name': 'gompic', 'version': '2016.10'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + sources = [ 'v%(version)s.tar.gz', - lapack_src, + (lapack_src, lapack_unpack_cmd), large_src, timing_src, ] @@ -28,7 +33,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] -- GitLab From a6988303075209a266a8274b42cae137e307285c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 23:19:09 +0100 Subject: [PATCH 332/350] sync OpenBLAS easyconfig with #3795 --- .../OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb index 5a0c375e93..abbe566e01 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -14,9 +14,14 @@ toolchain = {'name': 'GCC', 'version': '4.9.4-2.25'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + sources = [ 'v%(version)s.tar.gz', - lapack_src, + (lapack_src, lapack_unpack_cmd), large_src, timing_src, ] @@ -28,7 +33,6 @@ source_urls = [ ] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] -- GitLab From e8fd6a87f7465e1d7f269aa82468c9f9827169a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 23:27:02 +0100 Subject: [PATCH 333/350] correctly update $CPATH in libxml2 easyconfig --- easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb | 2 ++ 1 file changed, 2 insertions(+) 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..e1e1cbadae 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 @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/libxml2/libxml'], } +modextrapaths = {'CPATH': ['include/libxml2']} + moduleclass = 'lib' -- GitLab From 60aaae03fc867e054deeeac601fbc04dd1e2bcfc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2016 23:44:31 +0100 Subject: [PATCH 334/350] include original download URL for ISL source tarball --- easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb | 1 + easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb | 1 + easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 1 + easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 1 + easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 1 + 20 files changed, 20 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb index 97ecab725e..51246f2bf5 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb @@ -16,6 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb index 0cc4d2d8be..497c0a4c85 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb @@ -16,6 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb index 76ee08688e..c0547aecc5 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb @@ -16,6 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb index 8f71a86f5f..6e2d418981 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb @@ -16,6 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb index a553c070ef..36f8d8681c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb @@ -16,6 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb index 7dd0f5df24..848f51df6b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb @@ -16,6 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb index f77a70efc3..799e61d8cc 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb @@ -18,6 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb index 9974833bba..fc3c2e200b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb @@ -18,6 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb index a3c67d644e..ae2943aa4a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb @@ -18,6 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb index b78ac53014..b25525fd47 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb @@ -18,6 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb index 0906283ab2..93f5790d42 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb @@ -18,6 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb index 1af6bd9c36..4745dd6247 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb @@ -18,6 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index 8bbf0ea88e..efb1b05bd5 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -19,6 +19,7 @@ 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://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index a69c58da2c..4a102e1afe 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -16,6 +16,7 @@ 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://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb index c25b63f7b1..28110f5c07 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -16,6 +16,7 @@ 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://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb index 83ebb4cb78..58026e971a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb @@ -16,6 +16,7 @@ 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://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index 1f2fc04edb..151877d38d 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -18,6 +18,7 @@ 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://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index ac9aa8567c..e03a15a183 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ 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://isl.gforge.inria.fr/', # original HTTP source for ISL (isl-0.15.tar.bz2) dependency + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index 5b9af4041a..908db129dc 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -19,6 +19,7 @@ source_urls = [ 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror 'https://ftp.gnu.org/gnu/gcc/gcc-%(version)s/', # Alternative GCC + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index a375f0e539..88ea84242b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -18,6 +18,7 @@ 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://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ -- GitLab From 957c1c35bb24f15e88cbb1a1c7ca57d5c438245d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2016 00:00:29 +0100 Subject: [PATCH 335/350] fix/sync copyright/author headers in GROMACS 2016 easyconfigs --- .../GROMACS/GROMACS-2016-foss-2016b-hybrid.eb | 11 ++++------- .../g/GROMACS/GROMACS-2016-foss-2016b-mt.eb | 19 ++++++++----------- 2 files changed, 12 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb index be709c1c8d..f72c224d32 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb @@ -1,18 +1,15 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University / The Francis Crick Institute +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute # Authors:: -# * Wiktor Jurkowski -# * Fotis Georgatos +# * Wiktor Jurkowski +# * Fotis Georgatos # * George Tsouloupas # * Kenneth Hoste # * Adam Huffman # License:: MIT/GPL -# -# Version 5.1.4 -# Author: Adam Huffman -# The Francis Crick Institute ## name = 'GROMACS' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb index b1fa93887b..1a85f392c7 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb @@ -1,18 +1,15 @@ ## # 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 +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman # 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' -- GitLab From a070233bd4d8e6bcfbe79b453e52f191c0e3f554 Mon Sep 17 00:00:00 2001 From: eediaz1987 Date: Tue, 15 Nov 2016 00:49:03 +0100 Subject: [PATCH 336/350] Update x265-1.9-goolf-1.7.20.eb --- easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb b/easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb index 44548e3d8d..f346f0f6b3 100644 --- a/easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/x265/x265-1.9-goolf-1.7.20.eb @@ -12,9 +12,11 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['http://ftp.videolan.org/pub/videolan/x265/'] sources = ['x265_%(version)s.tar.gz'] -builddependencies = [('CMake', '2.8.11')] +builddependencies = [ + ('CMake', '3.5.2') +] dependencies = [ - ('Yasm','1.3.0'), + ('Yasm','1.3.0'), ] start_dir = 'source' -- GitLab From b94bb016a7c6342580ea35773618d8d4b113b3db Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 14 Nov 2016 21:50:25 -0500 Subject: [PATCH 337/350] Add forgotten mpi_mic removing dependency patch file for ifort 2016.*. --- .../i/ifort/ifort_2016_no_mpi_mic_dependency.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/i/ifort/ifort_2016_no_mpi_mic_dependency.patch diff --git a/easybuild/easyconfigs/i/ifort/ifort_2016_no_mpi_mic_dependency.patch b/easybuild/easyconfigs/i/ifort/ifort_2016_no_mpi_mic_dependency.patch new file mode 100644 index 0000000000..6c852c220d --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort_2016_no_mpi_mic_dependency.patch @@ -0,0 +1,13 @@ +Eliminate dependency on intel-mpi-rt-mic which in turn brings in intel-mpi-rt. +author: Bart Oldeman (McGill HPC) +--- pset/mediaconfig.xml.orig 2016-11-14 12:57:14.214649000 -0500 ++++ pset/mediaconfig.xml 2016-11-14 12:57:30.108947210 -0500 +@@ -1758,7 +1758,7 @@ + ${PACKAGE_DIR}/rpm + rpm + +- ++ + Intel Fortran Compiler for Intel(R) 64 + Intel(R) Fortran Compiler 16.0 Update 2 + インテル(R) Fortran コンパイラー (インテル(R) 64) -- GitLab From fe96fa72a1ecbde7c169b05bcac6c4df0cec7d2d Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 14 Nov 2016 21:56:55 -0500 Subject: [PATCH 338/350] Apply no_mpi_mic_dependency patch to forgotten ifort-2016.* easyconfig. --- .../easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index d331cd8e4a..1f89b45357 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -10,6 +10,9 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2016_no_mpi_mic_dependency.patch'] + checksums = ['bce7f6a71f7e44f67956197501d00b7c'] gccver = '4.9.3' -- GitLab From e0e1ce0f884fd0d8fc4c43f2cbe2b150dd517dd9 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 15 Nov 2016 11:19:58 +0400 Subject: [PATCH 339/350] commiting --- .../g/gencore_variant_detection/gencore_variant_detection-1.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb index 9cf70a3ec4..b18b2dba0a 100644 --- a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb +++ b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb @@ -28,6 +28,7 @@ builddependencies = [('Anaconda3', '4.0.0')] #environment_file = sources[0] #remote_environment = "nyuad-cgsb/gencore_variant_detection_1.0" +preinstallopts = "conda install -f -c conda conda-env=2.5.2 && " remote_environment = "nyuad-cgsb/%(name)s_%(version)s" sanity_check_paths = { -- GitLab From 9c8f9c47e6b6a4d6b66577470dcb639c306d3545 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 15 Nov 2016 12:20:03 +0400 Subject: [PATCH 340/350] commiting --- easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb | 2 ++ easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb index 7f580ea182..49db3e8b28 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -16,4 +16,6 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['31ed3ef07435d7068e1e03be49381b13'] +postinstallcmds = ["conda install -f -c conda conda-env=2.5.2"] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb index 9d77e1debf..a9a1448d38 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb @@ -16,4 +16,6 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['546d1f02597587c685fa890c1d713b51'] +postinstallcmds = ["conda install -f -c conda conda-env=2.5.2"] + moduleclass = 'lang' -- GitLab From 42d2669084a54ada36635a6a26d80c2f5d842e32 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2016 09:56:30 +0100 Subject: [PATCH 341/350] prefix 'conda install' post install command with update to $PATH so conda is found --- easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb | 2 +- easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb index 49db3e8b28..c05c115ad0 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -16,6 +16,6 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['31ed3ef07435d7068e1e03be49381b13'] -postinstallcmds = ["conda install -f -c conda conda-env=2.5.2"] +postinstallcmds = ["PATH=%(installdir)s/bin:$PATH conda install -f -c conda conda-env=2.5.2"] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb index a9a1448d38..3ddab5e86a 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb @@ -16,6 +16,6 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['546d1f02597587c685fa890c1d713b51'] -postinstallcmds = ["conda install -f -c conda conda-env=2.5.2"] +postinstallcmds = ["PATH=%(installdir)s/bin:$PATH conda install -f -c conda conda-env=2.5.2"] moduleclass = 'lang' -- GitLab From 01251230681df48ffb31050481f6ec75ef67effb Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 15 Nov 2016 12:59:31 +0400 Subject: [PATCH 342/350] updating anaconda blocks with postinstallcmds --- easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb index 49db3e8b28..2888ffe699 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -18,4 +18,5 @@ checksums = ['31ed3ef07435d7068e1e03be49381b13'] postinstallcmds = ["conda install -f -c conda conda-env=2.5.2"] + moduleclass = 'lang' -- GitLab From 44a4fa61c04063e01e26c0e10abef36173d3b40f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2016 10:00:14 +0100 Subject: [PATCH 343/350] remove preinstallopts from gencore_variant_detection easyconfig --- .../gencore_variant_detection/gencore_variant_detection-1.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb index bad5214152..b799146d37 100644 --- a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb +++ b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb @@ -23,8 +23,6 @@ toolchain = {'name': 'dummy', 'version': ''} builddependencies = [('Anaconda3', '4.0.0')] -preinstallopts = "conda install -f -c conda conda-env=2.5.2 && " - # Use one of the following - either an environment.yml file or a remote environment definition #environment_file = '/path/to/conda-environment.yml' remote_environment = "nyuad-cgsb/%(name)s_%(version)s" -- GitLab From 4b7a8240553e93f4b01ea27daab0eefeddf1d25f Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 15 Nov 2016 13:02:06 +0400 Subject: [PATCH 344/350] removing preinstallopts from gencore --- .../gencore_variant_detection/gencore_variant_detection-1.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb index bad5214152..b799146d37 100644 --- a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb +++ b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb @@ -23,8 +23,6 @@ toolchain = {'name': 'dummy', 'version': ''} builddependencies = [('Anaconda3', '4.0.0')] -preinstallopts = "conda install -f -c conda conda-env=2.5.2 && " - # Use one of the following - either an environment.yml file or a remote environment definition #environment_file = '/path/to/conda-environment.yml' remote_environment = "nyuad-cgsb/%(name)s_%(version)s" -- GitLab From c46af2266710a67ff56a211635241e0aa1336d91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2016 11:01:16 +0100 Subject: [PATCH 345/350] specify installation directory in postinstallcmd --- easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb | 2 +- easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb index 3ea02d05f6..dff49570f3 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -16,7 +16,7 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['31ed3ef07435d7068e1e03be49381b13'] -postinstallcmds = ["PATH=%(installdir)s/bin:$PATH conda install -f -c conda conda-env=2.5.2"] +postinstallcmds = ["PATH=%(installdir)s/bin:$PATH conda install -f -p %(installdir)s -c conda conda-env=2.5.2"] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb index 3ddab5e86a..2e63871ba7 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb @@ -16,6 +16,6 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['546d1f02597587c685fa890c1d713b51'] -postinstallcmds = ["PATH=%(installdir)s/bin:$PATH conda install -f -c conda conda-env=2.5.2"] +postinstallcmds = ["PATH=%(installdir)s/bin:$PATH conda install -f -p %(installdir)s -c conda conda-env=2.5.2"] moduleclass = 'lang' -- GitLab From b5f81b4ce4fb104c11a86c0d19c47ef1829c0c2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2016 11:37:17 +0100 Subject: [PATCH 346/350] install conda 4.2.12 rather than coda-env 2.5.2 in postinstallcmds --- easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb | 5 +++-- easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb | 4 +++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb index dff49570f3..c0ff978ea5 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -16,7 +16,8 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['31ed3ef07435d7068e1e03be49381b13'] -postinstallcmds = ["PATH=%(installdir)s/bin:$PATH conda install -f -p %(installdir)s -c conda conda-env=2.5.2"] - +# a newer version of conda is required to run 'conda env create -p' +prep_env = "PATH=%(installdir)s/bin:$PATH " +postinstallcmds = [prep_env + "conda install -f -p %(installdir)s -c conda conda=4.2.12 ruamel_yaml=0.11.14"] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb index 2e63871ba7..87325e0a06 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb @@ -16,6 +16,8 @@ source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] checksums = ['546d1f02597587c685fa890c1d713b51'] -postinstallcmds = ["PATH=%(installdir)s/bin:$PATH conda install -f -p %(installdir)s -c conda conda-env=2.5.2"] +# a newer version of conda is required to run 'conda env create -p' +prep_env = "PATH=%(installdir)s/bin:$PATH " +postinstallcmds = [prep_env + "conda install -f -p %(installdir)s -c conda conda=4.2.12 ruamel_yaml=0.11.14"] moduleclass = 'lang' -- GitLab From a25de62376f0bf3ebdecd6e8aa62baa0fe4fa81b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2016 11:56:16 +0100 Subject: [PATCH 347/350] disable installing libiberty for binutils built with intel toolchain --- easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 7598e76c07..2c7152bf01 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -13,6 +13,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# libiberty doesn't seem to compile with Intel compilers +install_libiberty = False + # disable warning/error #175 ("subscript out of range") buildopts = 'CFLAGS="$CFLAGS -wd175"' -- GitLab From 62d554bcf80e059b228cb0fb62458e894d85d326 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2016 12:49:20 +0100 Subject: [PATCH 348/350] fix directory name for perl-app-cpanminus easyconfigs --- .../perl-app-cpanminus-1.7039.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/{perl_app_cpanminus => perl-app-cpanminus}/perl-app-cpanminus-1.7039.eb (100%) diff --git a/easybuild/easyconfigs/p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb similarity index 100% rename from easybuild/easyconfigs/p/perl_app_cpanminus/perl-app-cpanminus-1.7039.eb rename to easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb -- GitLab From 6b4bd2a0fe1880fd51e3d41788dc864819b15640 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2016 13:58:14 +0100 Subject: [PATCH 349/350] add README for archived easyconfigs --- easybuild/easyconfigs/__archive__/README | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 easybuild/easyconfigs/__archive__/README diff --git a/easybuild/easyconfigs/__archive__/README b/easybuild/easyconfigs/__archive__/README new file mode 100644 index 0000000000..37371576b7 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/README @@ -0,0 +1,10 @@ +This directory contains archived easyconfig files. + +Reasons for archiving easyconfigs include: +* old/obsolete software versions +* use of deprecated toolchains + +These easyconfig may or may not work with current version of EasyBuild. They are no longer actively maintained, +and they are no longer included in the regression testing that is done for every new EasyBuild release. + +Use them with care, and consider to use more recent easyconfigs for the respective software packages instead. -- GitLab From 218ab0dfd94bb4c1bf414d2c71aeb8c97992599c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2016 15:03:09 +0100 Subject: [PATCH 350/350] bump version to 3.0.0, update release notes --- RELEASE_NOTES | 62 ++++++++++++++++++++++++++++++++++++++++++++++++--- setup.py | 2 +- 2 files changed, 60 insertions(+), 4 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index c74d917ce1..0a73a07315 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,64 @@ 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 7,060 easyconfig files, for 1,085 different software packages, -37 different (compiler) toolchains, 13 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 6,176 easyconfig files, for 1,116 different software packages, +25 different (compiler) toolchains, 13 software bundles and 1 meta-package. + + +v3.0.0 (November 16th 2016) +--------------------------- + +feature release +- backwards incompatible changes: + - archive easyconfigs using old inactive toolchains + - see #3725, #3728, #3729, #3730, #3731, #3732, #3733, #3735, #3736, #3737, #3738 + - only taken into account by EasyBuild if --consider-archived-easyconfigs is enabled + - no easyconfigs available outside of archive for QLogicMPI + 15 toolchains: + - ClangGCC, cgmpich, cgmpolf, cgmvapich2, cgmvolf, cgompi, cgoolf, gmacml, + goalf, gpsmpi, gpsolf, iiqmpi, intel-para, ipsmpi, iqacml + - fix name in PyTables easyconfigs (was pyTables) (#3785) +- added example easyconfig files for 32 new software packages: + - 3to2 (#3655), Anaconda2 (#3337), Anaconda3 (#3337), ART (#3724), atools (#3631), + awscli (#3645), behave (#3751), Blosc (#3785), bokeh (#3790), Cantera (#3655), + Cargo (#3764), dadi v1.7.0, distributed (#3786), ea-utils (#3634), Elk (#3644), + FGSL (#3638), gencore_variant_detection (#3337), help2man (#3768), lbzip2 (#3791), + Log-Log4perl (#3574), Minimac2 (#3783), mypy (#3694), OBITools (#3573), + perl-app-cpanminus (#3337), PGDSpider (#3625), prokka (#3755), Reads2snp (#3609), + spglib-python (#3620), SUNDIALS (#3654, #3655), SelEstim (#3626), XMLStarlet (#3797), + x265 (#3090) +- added easyconfigs for new 'intelcuda' toolchain (#3750) +- added new easyconfigs for existing toolchains: + - goolfc/2016.08 (#3796), goolfc/2016.10 (#3666, #3775), intel/2017.00 (#3543), intel/2017.01 (#3757), + iomkl/2016.09-GCC-4.9.3-2.25 (#3680), iomkl/2016.09-GCC-5.4.0-2.26 (#3772) +- added additional easyconfigs for various supported software packages, including: + - Advisor 2017 update 1, Amber 16, ATLAS 3.10.2, GROMACS 2016, Octave 4.0.3, + OpenFOAM 3.0.1, PyTables 3.3.0, QuantumESPRESSO 6.0, Rust v1.12.1 +- various other enhancements, including: + - STREAM builds using ~56GiB and ~111GiB (#3670) +- various bug fixes, including: + - fix source spec in VASP easyconfig, ensure static linking with Intel MKL (#3381) + - fix source URL in GCCcore 6.2.0 easyconfig (#3608) + - correct STAMP dependency in i-cisTarget, must be 1.3 (#3613) + - consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#3623) + - fix source URLs for Cython (#3636) + - add Bison as build dep and M4 as runtime dep for flex 2.6.0 (#3656) + - enable parallel building of flex 2.6.0 (#3630) + - add zlib and bzip2 dependencies to X11 bundle (#3662) + - use 'letter_dir_for' function rather than just grabbing 1st letter of software name in easyconfigs tests (#3664) + - add patch to fix typo in GRIT 2.0.5 (#3675) + - fix typo in patch for WRF 3.8.0 (#3702) + - use $CC,$CXX rather than $I_MPI_CC,$I_MPI_CXX in patch for OpenFOAM 4.0 (#3703) + - patch FLTK to fix 'undefined symbol' issue when building Octave (#3704) + - include Pillow as a proper dep for scikit-image rather than as extension, since it has deps itself (#3723) + - update Travis config w.r.t. changes framework config defaults and required Lmod version (#3773) + - don't limit parallellism to 4 in recent GCC easyconfigs (#3776, #3777, #3778) + - include M4 as dependency in flex 2.5.39 easyconfigs + fix consistency issues (#3782) + - consistently apply patch for ncurses 6.0 (#3792) + - eliminate dependency on mpi-mic-rt in ifort (#3793) + - include Autotools as build dependency in all beagle-lib and MrBayes easyconfigs (#3794) + - make OpenBLAS use the LAPACK version specified in the easyconfig (v0.2.18 & v0.2.19) (#3795) + - include original download URL for ISL source tarball in GCC easyconfigs (#3798) + - disable installing libiberty for binutils built with intel toolchain (#3802) v2.9.0 (September 23rd 2016) ---------------------------- @@ -1048,7 +1104,7 @@ v0.8 (June 29th 2012) --------------------- - added support for building/installing 17 additional software packages: - - BEAGLE, Doxygen, g2clib, g2lib, HDF, HDF5, JasPer, libpng, Maple, + - BEAGLE, Doxygen, g2clib, g2lib, HDF, HDF5, JasPer, libpng, Maple, MrBayes, NCL, netCDF, netCDF-Fortran, Szip, WPS, WRF, zlib - the build procedure for WRF and WPS includes running the tests available for these packages - various bug fixes and enhancements: diff --git a/setup.py b/setup.py index f4cbb44d3b..97b6b01f04 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 = '3.0.0.dev0' +VERSION = '3.0.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab